It means threading a special tool into the bottom bracket shell that has cutters the shave metal off of the outside edges (faces) of the shell. I makes those faces accurately flat, exactly parallel to each other and at an exact 90° to the crank spindle. Usually only the slightest bit of metal is removed.

A similar device is used to "face" and square up the headtube to assure the headset is properly aligned with the headtube and fork steerer tube.