Novel 3D architecture of electronics packages raises immense challenges for electrical fault isolation and physical failure analysis (PFA). This paper describes a streamlined workflow involving 3D X-ray Microscopy (XRM) to effectively bridge fault isolation and physical failure analysis (PFA). The case studies on chip-to-chip micro-bump interconnecting failure will be discussed. X-ray microscopy improved the efficiency and efficacy of failure analysis (FA) by non-destructively imaging and analyzing the defects, which was impossible for traditional faulty isolation techniques.