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Over the past 75 years, microelectronic device miniaturization has been enabled by the development of novel materials and increasingly compact and complex device architectures. Rapid and ongoing evolution of advanced test capabilities is needed to support all aspects of hardware development, manufacturing, quality, security assurance and supply chain verification. Multi-modal and multi-scale test methodologies that build on existing trusted methodologies are needed to combat the array of increasingly sophisticated and diverse threats to device integrity. Advances in architecture place significant demands on metrology, particularly at the densely packed, multi-interface regions in advanced-node devices. Techniques such as scanning transmission electron microscopy (STEM) and atom probe tomography (APT) add to the existing suite of metrology techniques for physical assurance by providing sub-angstrom spatial resolution for detailed atomic-scale analysis. The efficacy of these and other techniques are inextricably linked to the preparation of high quality, representative electron transparent specimens in configurations suitable for each specific technique. Specimen preparation of features at this scale and geometric complexity is non-trivial. Physical constraints dictate that even a perfectly prepared specimen will inescapably contain multiple adjacent and overlapping features resulting in signal convolution when imaged in transmission. Margins for error and tolerance for artifact are vanishingly small considering that nanometer scale misplacement of site-specificity will exacerbate the signal convolution problem, in some cases completely obscuring key information. This paper addresses some of the challenges and physical limitations associated with locating, capturing, and isolating a nm scale feature of interest (FOI) within the volume of an ultra-thin electron transparent STEM specimen. We present a robust, ultra site-specific specimen preparation methodology using focused ion beam (FIB) optimized for STEM analysis, enabling high-resolution structural and chemical characterization of complex nanoscale interfaces with precise isolation of features of interest. Although the specific example presented focuses on the challenges of STEM specimen preparation for FinFET devices at the 4 nm technology node, the concepts presented have broad application to any geometrically complex material system.