MCS is an ASCII file. If you wish to program raw data you may need a raw file format, or convert it in your program.
Usually, raw file format are saved as '.bin'. Then, each bytes in the file is what you poke to the memory. You can select the output file format in your bitgen tool.
It depend on which tool you use to program the EEPROM. If you use a stand-alone programmer, the software that come with it usually can read many file format, and extract the EEPROM bytes from it. In any case, a file saved as '.bin' usually is the exact copy of what will be put into the EEPROM.