Surgical excision is the standard of care. Some individuals advocate the use of hair removal laser for the treatment of congenital nevi. While this is likely safe and effective for small congenital nevus, laser removal for larger lesions might pose a liability for the laser surgeon if malignancy developed from a deep (dermal) component of the nevus that is not reached by the laser. Repigmentation after laser treatment of congenital nevi or superficial curettage supports this concern.

Many are surgically removed for aesthetics and relief of psychosocial burden, but larger ones are also excised for prevention of cancer, although the benefit is impossible to assess for any individual patient. Proliferative nodules are usually biopsied and are regularly but not systematically found to be benign. Estimates of transformation into melanoma vary from 2-42% in the literature, but are most commonly considered to be at the low end of that spectrum due to early observer bias.

Treatment is usually supportive treatment, that is, treatment to reduce any symptoms rather than to cure the condition.

- Enucleation of the odontogenic cysts can help, but new lesions, infections and jaw deformity are usually a result.

- The severity of the basal-cell carcinoma determines the prognosis for most patients. BCCs rarely cause gross disfigurement, disability or death .

- Genetic counseling

The decision to observe or treat a nevus may depend on a number of factors, including cosmetic concerns, irritative symptoms (e.g., pruritus), ulceration, infection, and concern for potential malignancy.

Mole removal risks mainly depend on the type of mole removal method the patient undergoes. First, mole removal may be followed by some discomfort that can be relieved with pain medication. Second, there is a risk that a scab will form or that redness will occur. However, such scabs and redness usually heal within one or two weeks. Third, as in other surgeries, there is also risk of infection or an anesthetic allergy or even nerve damage. Lastly, the mole removal may imply an uncomfortable scar depending on the mole size.

In general, there is no treatment available for CMTC, although associated abnormalities can be treated. In the case of limb asymmetry, when no functional problems are noted, treatment is not warranted, except for an elevation device for the shorter leg.

Laser therapy has not been successful in the treatment of CMTC, possibly due to the presence of many large and deep capillaries and dilated veins. Pulsed-dye laser and long-pulsed-dye laser have not yet been evaluated in CMTC, but neither argon laser therapy nor YAG laser therapy has been helpful.

When ulcers develop secondary to the congenital disease, antibiotic treatment such as oxacillin and gentamicin administered for 10 days has been prescribed. In one study, the wound grew Escherichia coli while blood cultures were negative.

First, a diagnosis must be made. If the lesion is a seborrheic keratosis, then shave excision, electrodesiccation or cryosurgery may be performed, usually leaving very little if any scarring. If the lesion is suspected to be a skin cancer, a skin biopsy must be done first, before considering removal. This is unless an excisional biopsy is warranted. If the lesion is a melanocytic nevus, one has to decide if it is medically indicated or not

If a melanocytic nevus is suspected of being a melanoma, it needs to be sampled or removed and sent for microscopic evaluation by a pathologist by a method called skin biopsy. One can do a complete excisional skin biopsy or a punch skin biopsy, depending on the size and location of the original nevus. Other reasons for removal may be cosmetic, or because a raised mole interferes with daily life (e.g. shaving). Removal can be by excisional biopsy or by shaving. A shaved site leaves a red mark on the site which returns to the patient’s usual skin color in about two weeks. However, there might still be a risk of spread of the melanoma, so the methods of Melanoma diagnosis, including excisional biopsy, are still recommended even in these instances. Additionally, moles can be removed by laser, surgery or electrocautery.

In properly trained hands, some medical lasers are used to remove flat moles level with the surface of the skin, as well as some raised moles. While laser treatment is commonly offered and may require several appointments, other dermatologists think lasers are not the best method for removing moles because the laser only cauterizes or, in certain cases, removes very superficial levels of skin. Moles tend to go deeper into the skin than non-invasive lasers can penetrate. After a laser treatment a scab is formed, which falls off about seven days later, in contrast to surgery, where the wound has to be sutured. A second concern about the laser treatment is that if the lesion is a melanoma, and was misdiagnosed as a benign mole, the procedure might delay diagnosis. If the mole is incompletely removed by the laser, and the pigmented lesion regrows, it might form a recurrent nevus.

Electrocautery is available as an alternative to laser cautery. Electrocautery is a procedure that uses a light electrical current to burn moles, skin tags, and warts off the skin. Electric currents are set to a level such that they only reach the outermost layers of the skin, thus reducing the problem of scarring. Approximately 1-3 treatments may be needed to completely remove a mole. Typically, a local anesthetic is applied to the treated skin area before beginning the mole removal procedure.

For surgery, many dermatologic and plastic surgeons first use a freezing solution, usually liquid nitrogen, on a raised mole and then shave it away with a scalpel. If the surgeon opts for the shaving method, he or she usually also cauterizes the stump. Because a circle is difficult to close with stitches, the incision is usually elliptical or eye-shaped. However, freezing should not be done to a nevus suspected to be a melanoma, as the ice crystals can cause pathological changes called "freezing artifacts" which might interfere with the diagnosis of the melanoma.

Café au lait spots can be removed with lasers. Results are variable as the spots are often not completely removed or can come back after treatment. Often, a test spot is treated first to help predict the likelihood of treatment success.

As Becker's nevus is considered a benign lesion, treatment is generally not necessary except for cosmetic purposes. Shaving or trimming can be effective in removing unwanted hair, while electrology or laser hair removal may offer a longer-lasting solution. Different types of laser treatments may also be effective in elimination or reduction of hyperpigmentation, though the results of laser treatments for both hair and pigment reduction appear to be highly variable.

Surgical excision of a sebaceous cyst is a simple procedure to completely remove the sac and its contents.

There are three general approaches used: traditional wide excision, minimal excision, and punch biopsy excision.

The typical outpatient surgical procedure for cyst removal is to numb the area around the cyst with a local anaesthetic, then to use a scalpel to open the lesion with either a single cut down the center of the swelling, or an oval cut on both sides of the centerpoint. If the cyst is small, it may be lanced instead. The person performing the surgery will squeeze out the keratin surrounding the cyst, then use blunt-headed scissors or another instrument to hold the incision wide open while using fingers or forceps to try to remove the cyst intact. If the cyst can be removed in one piece, the "cure rate" is 100%. If, however, it is fragmented and cannot be entirely recovered, the operator may use curettage (scraping) to remove the remaining exposed fragments, then burn them with an electro-cauterization tool, in an effort to destroy them in place. In such cases the cyst may recur. In either case, the incision is then disinfected and, if necessary, the skin is stitched back together over it. A scar will most likely result.

An infected cyst may require oral antibiotics or other treatment before or after excision. If pus has already formed then incision and drainage should be done along with avulsion of cyst wall with proper antibiotics coverage.

An approach involving incision, rather than excision, has also been proposed.

The management of a nevus depends on the specific diagnosis, however, the options for treatment generally include the following modalities:

No treatment of seborrheic keratoses is necessary, except for aesthetic reasons. Since a slightly increased risk of localized infection caused by picking at the lesion has been described, if a lesion becomes itchy or irritated by clothing or jewelry, a surgical excision is generally recommended.

Small lesions can be treated with light electrocautery. Larger lesions can be treated with electrodesiccation and curettage, shave excision, or cryosurgery. When correctly performed, removal of seborrheic keratoses will not cause much visible scarring except in persons with dark skin tones.

There is no treatment, but because this is a benign condition with no serious clinical complications, prognosis is excellent.

Sebaceous cysts generally do not require medical treatment. However, if they continue to grow, they may become unsightly, painful, infected, or all of the above.

Photodynamic therapy, cryotherapy (freezing), or local chemotherapy (with 5-fluorouracil) are favored by some clinicians over . Because the cells of Bowen's disease have not invaded the dermis, it has a much better prognosis than invasive squamous cell carcinoma.

Good results have been noted with the use of imiquimod for Bowen's disease, including on the penis (erythroplasia of Queyrat), although imiquimod is not (as of 2013) approved by the U.S. Food and Drug Administration for the treatment of any type of squamous cell carcinoma, and serious side effects can occur with use of imiquimod.

Large and especially giant congenital nevi are at higher risk for malignancy degeneration into melanoma. Because of the premalignant potential, it is an acceptable clinical practice to remove congenital nevi electively in all patients and relieve the nevocytic overload.

Many treatments have been tried for port-wine stains including freezing, surgery, radiation, and tattooing; port-wine stains can also be covered with cosmetics.

Lasers may be able to destroy the capillaries without significant damage to the overlying skin. Lasers and other light sources may therefore be able to reduce the redness of stains, although there is not enough evidence to recommend one form over another.

For most people in trials of pulsed dye laser, more than 25% of the redness was reduced by laser after one to three treatments. Adverse effects were rare in these trials, although some people had changes to the color of the skin, especially Chinese people with darker skin. There can be pain, crusting, and blistering in the two weeks after treatment. The trials only followed people for six months, so long-term outcomes are not known. Up to 10 treatments may be necessary for improvement, but complete removal may not result.

The use of topical rapamycin as an adjunct to pulsed dye laser may improve results.

Treatment is generally given before one year of age. However, as it is recommended to be performed under anesthesia (15 minutes) on small children, it is not always possible to get frequent treatments. For example in Finland a child gets treated 2-3 times per year, resulting in a target of "being ready before school age" (7 years) "(needs citation)".

After the laser treatment the skin is filled with black marks, the size of a pen. This is due to the laser instrument's size; the black marks disappear within 1–3 weeks. The treated area can be sore and swollen for a couple of days.

Radiation therapy can be delivered either as external beam radiotherapy or as brachytherapy (internal radiotherapy). Although radiotherapy is generally used in older patients who are not candidates for surgery, it is also used in cases where surgical excision will be disfiguring or difficult to reconstruct (especially on the tip of the nose, and the nostril rims). Radiation treatment often takes as few as 5 visits to as many as 25 visits. Usually, the more visits scheduled for therapy, the less complication or damage is done to the normal tissue supporting the tumor. Radiotherapy can also be useful if surgical excision has been done incompletely or if the pathology report following surgery suggests a high risk of recurrence, for example if nerve involvement has been demonstrated. Cure rate can be as high as 95% for small tumor, or as low as 80% for large tumors. Usually, recurrent tumors after radiation are treated with surgery, and not with radiation. Further radiation treatment will further damage normal tissue, and the tumor might be resistant to further radiation. Radiation therapy may be contraindicated for treatment of nevoid basal-cell carcinoma syndrome. The 2008 study reported that radiation therapy is a good treatment for primary BCCs and recurrent BCCs, but not for BCCs that have recurred following previous radiation treatment.

Photodynamic therapy (PDT) is a new modality for treatment of basal-cell carcinoma, which is administrated by application of photosensitizers to the target area. When these molecules are activated by light, they become toxic, therefore destroy the target cells. Methyl aminolevulinate is approved by EU as a photosensitizer since 2001. This therapy is also used in other skin cancer types. The 2008 study reported that PDT was a good treatment option for primary superficial BCCs, reasonable for primary low-risk nodular BCCs, but a 'relatively poor' option for high-risk lesions.

In the absence of successful treatment, hypertrophy (increased tissue mass) of the stains may cause problems later in life, such as loss of function (especially if the stain is near the eye or mouth), bleeding, and increasing disfigurement. Lesions on or near the eyelid can be associated with glaucoma. If the port-wine stain is on the face or other highly visible part of the body, its presence can also cause emotional and social problems for the affected person.

It is suggested that gene therapy might be used as a cure in the future.

Screening for melanoma in FAMMM kindreds should begin at age 10 with a baseline total body skin examination including scalp, eyes, oral mucosa, genital area, and nail, as family members may develop melanoma in their early teens.

At Mayo Clinic, FAMMM patients with a confirmed mutation and family history of pancreatic cancer are offered screening with either high-resolution pancreatic protocol CT, MRI, or endoscopic ultrasound starting at age 50 or 10 years younger than the earliest family member with pancreas cancer. They are counseled on the lack of evidence-based data to support screening, and on the limitations of our current technology to detect a lesion at a stage amenable to therapy.

A Q-switched laser has been successfully used to treat the condition.

Different therapeutic modalities have been attempted to repigment the lesions of nevus depigmentosus such as PUVA, excimer laser, and different grafting techniques. PUVA therapy has not been shown to be beneficial. Successful repigmentation was reported in a single case with 14 sessions of excimer laser treatment. Though the repigmentation of nevus depigmentosus is possible by grafting techniques, the results are inconsistent and recurrence is possible. In consideration of the experience of other authors and us, the quality and retention of pigment are unpredictable. These factors need to be considered while consulting and offering any treatment to the patient of nevus depigmentosus.

The most common treatment is the acne medication isotretinoin. It may be combined with prednisone. Dapsone, which is normally used to treat leprosy, is a riskier medication but is sometimes prescribed in cases where the normal therapy is ineffectual. Antibiotics such as tetracycline or erythromycin may also be prescribed. An alternative option is to treat with carbon dioxide laser therapy, followed by topical tretinoin therapy.

Surgery may be necessary to remove large nodules. Alternatively, nodules can be injected with corticosteroids such as triamcinolone.

Verruciform xanthoma is an uncommon benign lesion that has a verruciform (wart-like) appearance, but it may appear polypoid, papillomatous, or sessile. The verruciform was first described by Shafer in 1971 on the oral mucosa. Usually found on the oral mucosa of middle-aged persons, verruciform xanthomas have also been reported on the scrotum and penis of middle-aged to elderly Japanese males. While the most common site is the oral mucosa, lesions that occur elsewhere usually arise on the perineum or on the skin with some predisposing factor, such as lymphedema or an epidermal nevus.

Mucinous nevus (also known as "Nevus mucinosus") is a rare cutaneous condition characterized by hamartoma that can be congenital or acquired.