Paint Tool Sai, 1 - 3 layers for each piece, I usually merge them down once I am satisfied with what I have, and because I don't want to keep many different layers for this kind of work.
I might come back and retouch later, but first I want to practice a few things.
I also used Lazy Nezumi Pro for the basic isometry. You should check out this program if you get a chance.
