This is an old revision of the document!
Detailed overview of the entire process. Highly recommended.
http://www.springerlink.com/content/w8568j6533634w74/fulltext.pdf
Has some history and current techniques.
http://www.gemes.com/company_info/reverse_engineering_complex_ASICS.pdf
Basic overview of IC RE process
http://www.ece.cmu.edu/~ee760/
Class with some web resources on how to convert logic gates to silicon masks