Thanks for your query at DoctorSpring.com
Genital warts are known to respond to flonida , however since your wife is not showing an improvement with it, it's wise to stop using it and attempt an alternate mode of treatment.
The other options would be Aldara cream which is a prescription based cream to be applied on the affected area five times a week at night. It's a very effective mode of treatment.
The other option as your doctor rightly mentioned would be burning out the lesion or laser. there is no pain since before the procedure, application of EMLA which is a local anaesthetic cream is advocated.
Hence it's a painless procedure. There are no side effects of the procedure since its a superficial procedure.
There will be be associated redness and scabbing after the procedure for a few days which is how the procedure works.
Please let me know if you have any queries.