I saw my doctor for genital warts and was prescribed imiquimod 5% cream I used it 3 times. Now swollen and burning in the area is it a chemical burn?

No. This isn't a chemical burn. It's probably a strong response to the medicine and this is fairly common. Since it's troubling enough to write us about, hold the medicine and phone your physician for guidance.
Yes.It is very. caustic to oral skin( that's how it kills the virus ).Be careful to "paint" the lesion,and nothing else.