A method for Transmission Electron Microscopy (TEM) sample creation. The use of a Scanning Electron Microscope (SEM)—Scanning Transmission Electron Microscope (STEM) detector in the dual-beam focused ion beam (FIB)/SEM allows a sample to be thinned using the FIB, while the STEM signal is used to monitor sample thickness. A preferred embodiment of the present invention can measure the thickness of or create TEM samples by using a precise endpoint detection method. Preferred embodiments also enable automatic endpointing during TEM lamella creation and provide users with direct feedback on sample thickness during manual thinning. Preferred embodiments of the present invention thus provide methods for endpointing sample thinning and methods to partially or fully automate endpointing.