A method is provided of reducing the thickness of a region of a target sample. Reference data is obtained that is representative of x-rays generated by a particle beam being directed upon part of a reference sample under a first set of beam conditions. Under a second set of beam conditions the particle beam is directed upon the region of the target sample. The resultant x-rays are monitored as monitored data. Output data are then calculated based upon the reference and the monitored data. Material is then removed from the region, so as to reduce its thickness, in accordance with the output data.