The automation of TEM imaging and lamella preparation using focused ion beam (FIB) technology has gained significant momentum, particularly in the development of microprocessors. A key requirement of automating TEM sample preparation is ensuring consistent thickness control and accurate targeting of features of interest in the ultra-thin lamella. This work examines the factors that impact both metrics. It explains how FIB pattern calibration requires milling to be divided into steps to minimize the effects of drift, how the height of the protective cap on the ion-beam tip influences sample thickness, and how FIB aperture erosion has little impact on lamella thickness until it reaches a certain point where the lamella profile cannot be reliably maintained. It was also found that the tail of the ion beam remains invariant during aperture degradation in the operable range and that it plays a prominent role in determining the cross-sectional thickness of the TEM lamella.