A microscopy system for imaging a sample can include a scanning electron microscope system configured for imaging a surface layer of the sample and a focused ion beam system configured for generating an ion beam for milling the surface layer away from a sample after it has been imaged. A movable mechanical shutter can be configured to be moved automatically into a position between the sample and the scanning electron microscope system, so that when the electron beam is not imaging the sample the movable mechanical shutter is positioned between the sample and the scanning electron microscope system.