Raw binary file format

The meaning of the configuration bitstream is undocumented. Besides a simple optional compression and a CRC consistency check, the configuration data can be expected as an image of various configuration bits distributed over the FPGA chip. Encryption is pointless without a key, you can review the configuration mechanism of Cyclone III LS familiy that provides AES encrypted configuration.

Although configuration data is quite complex, scientific studies have shown, that it's basically possible to reveal gate level logic information from it. I think, the topic has been discussed at Altera forum before.