A system and a method for protecting code are provided. Extraction of code to be protected takes place during an object-to-object transformation and that code is replaced with fake binary code. The extracted code to be protected may then be encrypted or otherwise obscured and stored in a separate region of an object file. A prior source-to-source file transformation can be provided to isolate and mark the code to be protected, and to inject additional source code to handle later decryption.