Having met him a couple times I can say he is very, very good at this. He's less methodical/disclpined and more "RE the entire chip by staying away for 3 days straight". He doesn't really use any software at all. He just spends days in Photoshop making hundreds of layers and mapping the thing out in his head. I don't think he's even had an automated imaging setup until recently (manually taking tens of photos of chip dies and autostitching them)
If you want another good talk look up "dmitry backside ic probing"