I can think of several ways to do this all depending on the amount and sizes of the maps:
The grid is most likely "fixed" meaning that the center of the grid is always at 0,0,0 in world space
- manual: simplest, make an editor where you can "mark" cells to be usable in the game
- semi/manual: make an editor where you mark areas (similar to collision/nav meshes) that can be used in the game, then the editor will figure out which cells fully fit inside those meshes. You could do this by checking for every cell if all 6 points are inside.
- automatic: the editor figures out what areas of of the visual meshes are around a certain height and then figures out which cells fully fit in there
Last 2 could be combined with the first to correct miscalculations by hand.