if it's a surface scratch, you can try using some rubbing compound (like from turtle wax or meguiars) to rub it off, but if it's down to aluminum, you can do the following:
you can sand it down to the primer coat of the aluminum, then clean it off with denatured alcohol, primer coat it (if you use krylon or duplicolor), sand that down and clean it off with denatured alcohol, and paint your final coat on it. then if you want, you can put a clearcoat on top of that to give it the auto finish. i'd make sure the surfaces are flat, smooth, and clean before you go on to the next coat of paint. this is a long and painstaking process, but it will give you a really good shine that you'll never regret. if you by some chance cut through or sand through the primer, you'll need to use some sort of adhesive paint if you're going to use duplicolor or krylon.
paintwize, i definitely recommend VHT, although that stuff is really really hard to spray on. the brake and caliper paint (which i used, although you may find a not-so-heat resisitant one to work just as well) is a self priming paint that will adhere to even bare aluminum 100% of the time when cured. ie, it will never ever chip off. just make sure you don't mix brands of paint. so if you use VHT, stick with VHT. you can find vht paint at some kragens, autozones, and any speed shop.
EDIT: google also helps for figuring out how to paint.
