Dremel and bit recommendation

If you are just cleaning up after milling, I'd just get a set of good files and a perhaps a jig saw (the manual one).

What are you making a chassis for? I might rethink the choice of material. You're talking about making a chassis that will be almost 5mm thick.

I'd consider something along the lines of 3mm or 4mm 7075 (depending on the application), which is a lot stronger than 6061. I, often times, find myself wishing that I had gone with 7075, rather than 6061.

If you look at the specs of many models of rc cars and trucks, you will find that 6061 is what they use in the cheaper RTR version and 7075 is what they use in the Pro version. 7075, is much more rigid than 6061.

Once you have the chassis done up, you might also want to consider having it type III anodized. The anodizing will put an abrasion resistant coating on the chassis to help to keep it from getting buggered up by the screws and bottoming out.