Focused ion beam (FIB) microscopy is an essential technique for the site-specific sample preparation of atom probe tomography (APT). The site specific APT and automated APT sample preparation by FIB have allowed increased APT sample volume. In the workflow of APT sampling, it is very critical to control depth of the sample where exact region of interest (ROI) for accurate APT analysis. Very precise depth control is required at low kV cleaning process in order to remove the damaged layer by previous high kV FIB process steps. We found low kV cleaning process with 5 kV and followed by 2kV beam conditions delivers better control to reached exact ROI on Z direction. This understanding is key to make APT sample with fully automated fashion.