The scar remover just masks the scars. There is a trick to get rid of all or most of the scars. Take your to the water and get him to stand in it. Then set a tree on fire and hold it up to your creature so he'll burn all over, which he doesn't since he's standing in water. When you have him severely blackened, heal him and most of the scars should be gone. It's been a while since I used this trick so I think that is how it works.
I prefer this method since it will leave some scars visiable. I think that a few scars add character to a creature. The scar remover is a file which replaces the scar file so scars and bruses will never show.
I dislike scars personally, they don't seem to add character so much as they look like glitches. I mean some scars look realistic enough, but most scars in my experience look like horrible, graphics wise, especially when they abruptly end creating a line.