A scanning electron microscopy system is disclosed. The system includes a sample stage configured to secure a sample having conducting structures disposed on an insulating substrate. The system includes an electron-optical column including an electron source configured to generate a primary electron beam and a set of electron-optical elements configured to direct at least a portion of the primary electron beam onto a portion of the sample. The system includes a detector assembly configured to detect electrons emanating from the surface of the sample. The system includes a controller communicatively coupled to the detector assembly. The controller is configured to direct the electron-optical column and stage to perform, with the primary electron beam, an alternating series of image scans and flood scans of the portion of the sample, wherein each of the flood scans are performed sequential to one or more of the imaging scans.