Printed Circuit Boards (PCBs) play a critical role in everyday electronic systems, therefore the quality and assurance of the functionality for these systems is a topic of great interest to the government and industry. PCB manufacturing has been largely outsourced to cut manufacturing costs in comparison with the designing and testing of PCBs which still retains a large presence domestically. This offshoring of manufacturing has created a surge in the supply chain vulnerability for potential adversaries to garner access and attack a device via a malicious modification. Current hardware assurance and verification methods are based on electrical and optical tests. These tests are limited in the detection of malicious hardware modifications, otherwise known as Hardware Trojans. For PCB manufacturing there has been an increase in the use of automated X-ray inspection. These inspections can validate a PCB’s functionality during production. Such inspections mitigate process errors in real time but are unable to perform highresolution characterization on multi-layer fully assembled PCBs. In this paper, several X-ray reconstruction methods, ranging from proprietary to open-source, are compared. The high-fidelity, commercial NRecon software for SkyScan 2211 Multi-scale X-ray micro-Tomography system is compared to various methods from the ASTRA Toolbox. The latter is an open-source, transparent approach to reconstruction via analytical and iterative methods. The toolbox is based on C++ and MEX file functions with MATLAB and Python wrappers for analysis of PCB samples. In addition, the differences in required imaging parameters and the resultant artifacts generated by planar PCBs are compared to the imaging of cylindrical biological samples. Finally, recommendations are made for improving the ASTRA Toolbox reconstruction results and guidance is given on the appropriate scenarios for each algorithm in the context of hardware assurance for PCBs.