There is no way to REMOVE scratches from aluminum panels.
I have tried everything that was suggested on here including car wax and brasso. The finish on the aluminum has little or no similar properties to car paint hence, CAR WAX DOES NOT WORK. After I purchased replacement body panels from WeLoveMacs dot com I tried using Brasso. It did not remove the the scratches as they are to deep. After about a month, the panel began to tarnish, and has a very odd sepia-like tinge to it! DO NOT USE BRASSO! Although expensive and impractical, if you are as anal as I am, the only foreseeable solution is to replace the scratched panels.