Martin Schobert has designed an open source software, called Degate, to help reverse-engineering hardware components.   The process is the following:

• You must first take pictures of the layout of the depassivated hip
• Degate will attempt to recognize standard cells image pattern matching.
• Degate attempts also to reconstruct the netlist of wires and vias (vias are electronic connection between different layers).
• Then, it can build the full or partial logical layout.

Of course, the better the quality of the initial pictures (for instance using a Focussed Ion Bean (FIB)), the easier (and better) the automated result.

Degate will not do all the job.  It is a software aid to reverse engineer.  In any case, at the end, you will have to understand what the logic layout does.  Degate is not a tool for script kiddies.  It requires a good knowledge of micro electronics.  You’re working at the transistor/cell level.

The site provides also an interesting repository of documentation related to IC reverse-engineering.

Lesson: As for software obfuscation, the less reused patterns in the design of the chip, the more robust to reverse-engineering.