1. A method for automatically preparing a semiconductor sample in a dual-beam charged particle system, the method comprising: positioning the dual-beam charged particle system with respect to a semiconductor die sample region of interest to be examined in a sample chamber; with focused ion beam (FIB) deposition, forming a first precision fiducial marker and one or more additional fiducial markers at desired locations with respect to the region of interest; acquiring a first scanning electronic microscope (SEM) image of the region of interest; retrieving computer aided design (CAD) data describing the region of interest; synthesizing a second SEM image from CAD data describing the region of interest; masking the one or more additional fiducial markers in the first SEM image and comparing the masked first SEM image and the second SEM image to determine a final correction offset for an actual position of the precision fiducial marker; applying the final correction offset to the location of the precision fiducial marker; based on the corrected location of the precision fiducial marker, adjusting the position of the FIB relative to the sample, and milling with the FIB to create a sample lamellae for examination.