Disclosed herein is a system for profiling holes in non-opaque samples. The system includes: (i) an e-beam source configured to project an e-beam into an inspection hole in a sample, such that a wall of the inspection hole is struck and a localized electron cloud is produced; (ii) a light sensing infrastructure configured to sense cathodoluminescent light, generated by the electron cloud; and (iii) a computational module configured to analyze the measured signal to obtain the probed depth at which the wall was struck. A lateral offset, and/or orientation, of the e-beam is controllable, so as to allow generating localized electron clouds at each of a plurality of depths inside the inspection hole, and thereby obtain information at least about a two-dimensional geometry of the inspection hole.