Abstract This paper discusses the development of an automated cell layer counting process for preparing 3D NAND flash memory samples for TEM analysis. In an initial proof-of-concept, several line markings were inscribed on the test device in evenly spaced intervals in order to evaluate its helpfulness for a human operator. A more automated procedure was then developed in which cell layers were counted to a desired target layer starting from a reference layer set by the operator. At that point, the operator could begin preparing the TEM sample.