You create maps in radiant (*.map).
During the compiling the Compiler creates the *.bsp and *.d3bsp files.
I am not 100 percent sure but i think one of them contains the geometry and the other the light informations.
In the final step they are compressed into the *.ff
You can easily follow the procedure when you keep an eye on the cmd window during the compile process.
when you take a look into cod2 mapping you will notice that there was no *.ff, the game used the *.d3bsp to load the map.
(please correct me when i am wrong, it's quite a while that i mapped and took a look into the single steps, eapecially cod2)