A method of operating a particle beam microscopy. A particle beam is scanned across a scanning region of a surface of the object. Particles are detected by a detector system for a plurality of impingement locations of the primary beam within the scanning region. A detector system generates detector signals which represent for each of the impingement locations an intensity of the detected particles. Material data of the interaction regions are calculated depending on the detector signals and depending on topography data, which represent a topography of the object surface in the scanning region.