A scanning electron microscopy system may include an electron-optical sub-system and a controller. The electron-optical sub-system may include an electron source and an electron-optical column configured to direct an electron beam to a sample. The electron-optical column may include a double-lens assembly, a beam limiting aperture disposed between a first and second lens of the double-lens assembly, and a detector assembly configured to detect electrons scattered from the sample. In embodiments, the controller of the scanning electron microscopy system may be configured to: cause the electron-optical sub-system to form a flooding electron beam and perform flooding scans of the sample with the flooding electron beam; cause the electron-optical sub-system to form an imaging electron beam and perform imaging scans of the sample with the imaging electron beam; receive images acquired by the detector assembly during the imaging scans; and determine characteristics of the sample based on the images.