27c3: Reverse Engineering the MOS 6502 CPU (en)

There's a lot of information about reverse engineering some of the older CPUs around e.g. the MOS6502 (NES, Apple II, C64, etc). This is a great presentation showing how this CPU is reverse engineered: [this video] Basically it comes down to the fact that you can't really hide transistors and ultimately that's something you can reconstruct. It sounds like a lot of work, and it is, but if you do it you can perfectly emulate a chip. If you can dig out non volatile memory then potentially you have the firmware. Once someone has their hands on that it'll be broken, almost guaranteed, as it becomes a software problem. Lots of people are very good at assembly hacking.

If you have no experience in digital electronics at all, I would actually start with a book like Code by Charles Petzold. It's a pop-science book about electronics and goes from light bulbs and switches to simple logic blocks like adders. It covers the basic building blocks of virtually every cpu in existence - how to turn transistors into calculators. It's well written and provides some context to otherwise pretty dry textbooks. There is quite a bit of difference between how an FPGA works and is programmed versus a totally custom chip. You could also take a look at reverse engineering walkthroughs eg Ken Shirrif has a few on his blog. Nand2tetris is another good thing to look at. Finally, reverse engineering the MOS6502: [this video]