This is the second of the four main compiling programs. It takes the info from the .pt0 file from CSG and makes a .pt1 file for VIS by preparing clip planes, leafs and portals. It also checks for leaks.
More info from DOE, Snowdog: BSP: The BSP tool is the one that actually converts the .map file data into a useable .bsp file that the game engine can load. Once the BSP tool is run the map is essentially playable with the exception that it will have no visibility matrix and will have no lighting at all. Those crucial features are applied by the next two tools VIS and RAD.