X-ray computed tomography (XCT) offers a promising non-destructive method to assess high value components that are additively manufactured (AM) for space-based imaging. However, AM components can be often challenging to measure and the true resolution of the XCT system used is both non-trivial to determine and may change locally. To solve this, we used high precision micro-machining to manufacture a cylindrical reference pin with internal holes. This pin can then be inserted into any component via subtractive machining, prior to the XCT process. A pre-existing AM flexure is modified to allow our modular system to be implemented. This allows XCT scanning and porosity analysis of similar components (similar geometry and manufacturing process) to be refined and adjusted based on the known internal micro-machined hole size. Analysis of the XCT volumetric data is implemented using a Python script developed for Avizo 2022.1, to compare and suggest the ideal threshold grey value (GV). The plugin threshold comparison is semi-automatic and 15 times faster than a manual comparison. Study findings showed how different calibrated micro-machined hole sizes (30 μm–120 μm) needed different thresholding values (188 GV–195 GV). Challenges and future studies related to traceability of the suggested method are discussed.