A user interface for operation of a scanning electron microscope device that combines lower magnification reference images and higher magnification images on the same screen to make it easier for a user who is not used to the high magnification of electron microscopes to readily determine where on the sample an image is being obtained and to understand the relationship between that image and the rest of the sample. Additionally, other screens, such as, for example, an archive screen and a settings screen allow the user to compare saved images and adjust the settings of the system, respectively.