Definitive diagnosis can only occur with positive identification of the larvae. This involves radiologic imaging (preferably MRI which can reveal larval migration tracks and in some cases the larvae themselves) as well as surgical exploration during which larvae can be removed and examined for identification. Identification of exact species is often impossible as the instars of the various "Cuterebra" and "Trychoderma" spp. exhibit significant resemblance, but identification as a "Cuterebra" bot fly is sufficient for diagnosis as cuterebriasis. Typically, a third larval instar is found and identifiable by its dark, thick, heavily spined body.

Subcutaneous cysts may be surgically opened to remove less mature bots. If more matured, cysts may be opened and "cuterebra" may be removed using mosquito forceps. Covering the pore in petroleum jelly may aide in removal. If larvae are discovered within body tissues, rather than subcutaneously, surgical removal is the only means of treatment. Ivermectin may be administered with corticosteroids to halt larval migration in cats presenting with respiratory cuterebriasis, but this is not approved for use in cats. There is not yet a known cure for cerebrospinal cuterebriasis.