A system for scanning a plurality of regions of interest of a substrate using one or more charged particle beams, the system comprises: an irradiation module having charged particle optics; a stage for introducing a relative movement between the substrate and the charged particle optics; an imaging module for collecting electrons emanating from the substrate in response to a scanning of the regions of interest by the one or more charged particle beams; and wherein the charged particle optics is arranged to perform countermovements of the charged particle beam during the scanning of the regions of interest thereby countering relative movements introduced between the substrate and the charged particle optics during the scanning of the regions of interest.