Put the MP in a room with no windows. Turn the lights off.
BAM! No more scratches!
Apart from that the least extensive procedure you could try is polish, just don't rub too hard. The more extreme options include re-casing the whole computer, or having the case sanded down/stripped and re-anodised (probably not worth it, but if you did do this I would take it to a professional and have the whole case done in a different color, maybe matt black, or a blue). Most anodizing shops would be able to chemically strip the anodization off, but depending on what kind of aluminum the case is made from it may be more difficult than it is worth.