(My source for this was the mayo clinic website)

Medications
Genital warts treatments that can be applied directly to your skin include:

• Imiquimod (Aldara). This cream appears to boost your immune system's ability to fight genital warts. Avoid sexual contact while the cream is on your skin. It may weaken condoms and diaphragms and may irritate your partner's skin.
• Podofilox (Condylox). Podofilox works by destroying genital wart tissue. Your doctor may want to administer the first application, and will recommend precautionary steps to prevent the medication from irritating surrounding skin. Never apply podofilox internally. Additionally, this medication isn't recommended for use during pregnancy.
• Trichloroacetic acid, or TCA. This chemical treatment burns off genital warts. TCA must always be applied by a doctor.

Don't try to treat genital warts with over-the-counter medications. These medications aren't intended for use in the moist tissues of the genital area. Using over-the-counter medications for this purpose can cause even more pain and irritation.

Surgery
Surgery may be necessary to remove larger warts, warts that don't respond to medications, or - if you're pregnant - warts that your baby may be exposed to during delivery. Surgical options include:

• Freezing with liquid nitrogen (cryotherapy). Freezing works by causing a blister to form around your wart. As your skin heals, the lesions slough off, allowing new skin to appear. You may need repeated cryotherapy treatments.
• Electrocautery. This procedure uses an electrical current to burn off warts.
• Surgical excision. Your doctor may use special tools to cut off warts. You'll need local anesthesia for this treatment.
• Laser treatments. This approach, which uses an intense beam of light, can be expensive and is usually reserved for very extensive and tough-to-treat warts.