I guess a way to go is to ask the doctor what the mark is, when he says a scar, ask if you can remove it. You could tell him that you don't want future partners to mistake the scar for an STD.
There seems to be solutions to any cosmetic issue, but I would recommend discussing treatment with a doctor or dermatologist. The risk of further probelems from home treatment is too great!
I pointed out a mark on my penis that the doctor identified as a small scar. He indicated that it could be removed, but did not recommend a cosmetic procedure. I was mostly concerned with HPV and didn't follow up.
I mean I wouldn't mind...