A multi-column assembly for a scanning electron microscopy (SEM) system is disclosed. The multi-column assembly includes a plurality of electron-optical columns arranged in an array defined by one or more spacings. Each electron-optical column includes one or more electron-optical elements. The plurality of electron-optical columns is configured to characterize one or more field areas on a surface of a sample secured on a stage. The number of electron-optical columns in the plurality of electron-optical columns equals an integer number of inspection areas in a field area of the one or more field areas. The one or more spacings of the plurality of electron-optical columns correspond to one or more dimensions of the inspection areas.