A scanning electron microscopy system is disclosed. The system includes a multi-beam scanning electron microscopy (SEM) sub-system. The SEM sub-system includes a multi-beam electron beam source configured to generate a plurality of electron beams, a sample stage configured to secure a sample, an electron-optical assembly, and a detector assembly configured to detect a plurality of electron signal beams emanating from the surface of the sample to form a plurality of images, each image associated with an electron beam of the plurality of electron beams. The system includes a controller configured to receive the images from the detector assembly, compare two or more of the images to identify common noise components present in the two or more images, and remove the identified common noise components from one or more images of the plurality of images.