I hear your concerns, as I have had genital warts for just over a year now. One thing I have found in speaking to others with genital warts is that some treatments can cause the skin to be irritated and even white when applied too often or if you don't clean away the treatment after a few hours.
There is a pretty good article on genital warts here: http://www.cdc.gov/std/treatment/2010/genital-warts.htm
Personally, I use a product called Wartrol. Like you said, sometimes after the warts go away they can leave scars. However, since using Wartrol I have had no such scars. I recently wrote about my treatment at getridofgenitalwarts.net
Check it out if you are concerned about getting rid of your genital warts and returning your skin to its original state.
Best of luck,