Each of six scanning transmission electron microscope (STEM) system alignments were characterized with a sensitivity test to better understand the impact of the alignment on microscope automation for acquisition and metrology. The upper and lower limits of the alignment sensitivity combined with the accuracy of the automated system alignments are used to determine the process capability index (Cpk). The primary limiting factor for the alignment sensitivity was passing the metrology dynamic precision criteria of <0.3nm. Strong alignment offset showed impact on the autofunction robustness, but was marginal in comparison to the metrology sensitivity. All six of the STEM system alignments resulted in Cpk values greater than 1.3, supporting a three sigma quality process. Based on these results, criteria can be defined for alignment offset limits that will trigger automated preventative maintenance (APM) re-alignments and ensure that automated STEM metrology will meet the accuracy and precision requirements for adequate process control.