Most scratches are just in the laquer and you should have no problem rubbing it down. I've done the same with a set of Carbon aerobars to remove the decals. Just use a fine paper, I think I started with something like 400 and went on to 600. Keep stopping and checking, stop either when you get to the carbon itself (it's pretty obvious when you get there) or the scratch has disappeared (which ever comes first). I sprayed mine with a car laquer, just follow the instructions on the can and the finish is really very good.
On the other hand forks always get chipped, so you're fighting a losing battle if you want to keep them perfect and actually ride your bike.