Topographical data from a scanning probe microscope (5Pm) or similar device is used as a substitute for endpoint detection to allow accurate repair of defects in phase shift photomasks using a charged particle beam system (210-216). The topographical data from a defect area is used to create a display of a semitransparent topographical map (217), which can be superimposed over a charged particle beam image (218-222). The density of the topographical image and the alignment of the two images can be adjusted by the operator in order to accurately position the beam (224). Topographical data from an SPM can also be used to adjust charged particle beam dose for each point within the defect area based upon the elevation and surface angle at the particular point (225-230). The charge particle beam is then used to repair the defect (s) (232-234).