The manufacturing of custom-made anthropomorphic phantoms for X-ray studies has seen a significant increase in recent years, largely driven by the accessibility of 3D printing. Despite its commercial success, 3D printing faces unique challenges for niche and demanding applications such as accurate phantom fabrication. In this study, we focus on one of the initial sources of issues in achieving a gap-free phantom, the STL file from which it is manufactured. We propose an approach to address these issues and compare it with commonly used methods for exporting STL files from patient segmented data. Furthermore, we examined the resulting 3D printed phantom, both visually and through a clinical Computed Tomography (CT) imaging. The proposed approach demonstrated potential with resolving gaps and voids that are crucial for X-ray applications, but often overlooked in common STL exporting tools.