A variety of medications may be used to treat genital warts. Most of these medications are topical creams that are applied to the skin where the warts are located. Podofilox may be applied by your doctor to destroy the tissue in genital warts. Trichloroacetic acid is also applied by a doctor, and it burns off warts. Imiquimod may also be used, and it may encourage the immune system to destroy genital warts. If necessary, an interferon drug may be injected directly into the warts. Don't treat your genital warts with over-the-counter medications meant for other types of warts - this will only further irritate your skin. It's important to talk to your doctor to find the right medication for you.