Abstract: A separate user frame of reference is provided for the operator of an electron beam microscope to use in generating position and tilt commands for a motorized goniometer, rather than requiring that the operator input position and tilt commands to the motorized goniometer in the same frame of reference used by the goniometer to implement position and tilt changes. The electron beam image observed by the operator on a display screen furthermore forms the separate user frame of reference in order to make control of the specimen by the operator intuitive. Since the operator observes the user frame of reference and generates position and orientation commands in the user frame of reference, navigation around the sample is easy to accomplish, even for a novice operator. The image does not inadvertently rotate when other specimen movements are intended and an unintended modification in position along the beam axis does not occur for the imaged portion of the specimen unless the operator inputs such a modification.