Situating samples on an optical axis of a charged particle microscope can be performed based a 3D map of the samples. The 3D map is produced with back-side illumination of the samples and telecentric imaging to produce profile images. The profile images are a combined to form the 3D map. Using the 3D map, the processor is coupled to a sample stage to situate a selected sample or sample portion for imaging in the charged particle microscope. In some examples, the processor is responsive to selection of a sample using a graphical interface so that the sample stage is controlled to safely situate the selected sample without further operator intervention.