Administration of Podophyllin in HPV Treatment Clean the area before applying. Apply 0.5 g/day of podofilox gel directly to warts 2 times daily for 3 consecutive days. Continue this treatment for 4 weeks. Avoid applying it to the healthy tissue. Initial application should be 30-40 minutes while the second can be for 1-4 hours. Apply sparingly so it dries well. Remove the dried medicine with soap and water or alcohol. Do not apply the gel on large warts or many warts at once. Cover small patches one by one.