Reverse engineering of electronics systems is performed for various reasons ranging from honest ones such as failure analysis, fault isolation, trustworthiness verification, obsolescence management, etc. to dishonest ones such as cloning, counterfeiting, identification of vulnerabilities, development of attacks, etc. Regardless of the goal, it is imperative that the research community understands the requirements, complexities, and limitations of reverse engineering. Until recently, the reverse engineering was considered as destructive, time consuming, and prohibitively expensive, thereby restricting its application to a few remote cases. However, the advents of advanced characterization and imaging tools and software have counteracted this point of view. In this paper, we show how X-ray micro-tomography imaging can be combined with advanced 3D image processing and analysis to facilitate the automation of reverse engineering, and thereby lowering the associated time and cost. In this paper, we demonstrate our proposed process on two different printed circuit boards (PCBs). The first PCB is a four-layer custom designed board while the latter is a more complex commercial system. Lessons learned from this effort can be used to both develop advanced countermeasures and establish a more efficient workflow for instances where reverse engineering is deemed necessary.