Continued advancements in the architecture of 3D packaging have increased the challenges in fault isolation and failure analysis (FA), often requiring complex correlative workflows and multiple inference-based methods before targeted root cause analysis (RCA) can be performed. Furthermore, 3D package components such as through-silicon-vias (TSVs) and micro-bumps require sub-surface structural characterization and metrology to aid in process monitoring and development throughout fabrication and integration. Package road-mapping has also called for increased die stacking with decreased pitch, TSV size, and die thickness, and thus requires increased accuracy and precision of various stateof- the-art analytical techniques in the near future. Physical failure analysis (PFA), process monitoring, and process development will therefore depend on reliable, high-resolution data directly measured at the region of interest (ROI) to meet the complexity and scaling challenges. This paper explores the successful application of plasma-FIB (PFIB)/SEM techniques in 2D and 3D regimes and introduces diagonal serial sectioning at package scales as a novel approach for PFA and metrology. Both 2D and 3D analysis will be demonstrated in a high bandwidth memory (HBM) package case-study which can be applied more broadly in 3D packaging.