Hi,
Welcome to the ehealthforum and I am really glad to help you out. Your concern is regarding the warts that you are having on the penis.
For small warts, several medications(like podophyllum resin, Podofilox (Condylox), Trichloroacetic and bichloroacetic acids, Imiquimod 5% cream and interferons) are available, which can be applied directly to the surface of the warts. Other treatment options include surgical removal, Carbon dioxide laser treatment and electrodesiccation.
You can apply the topical treatment but apply it under medical supervision.
It is very difficult to precisely confirm a diagnosis without examination and investigations and the answer is based on the medical information provided. For exact diagnosis, you are requested to consult your doctor. I sincerely hope that helps. Take care.