Depends on how deep the scratches are. Meguiar's makes a Fender Care Kit that has a swirl remover in it that should take out most minor scratches from picks and so forth. Anything more than that and I'd probably buy some wet-and-dry sandpaper from an auto store and wet sand the guitar first, then use a scratch remover polish, a swirl remover, and finally a general car polish. I'd start with a 1000 grit sandpaper and move on to a 2000 grit paper.
I've done this kinda thing before, but I wouldn't consider myself an expert. You might wanna wait to see what the luthiers here have to say. :)