If you want to remove all the atoms 1 that lie “outside the map” (i.e. in low density) you can use
(trim-molecule-by-map imol-coords imol-map density-level delete/zero-occ?)
where delete/zero-occ? is 0 to remove the atoms and
1 to set their occupancy to zero.
There is a GUI interface for this feature under the “Extensions” menu item.