The accuracy of the 3D models created from medical scans depends on imaging hardware, segmentation methods and mesh processing techniques etc. The effects of geometry type, class imbalance, voxel and point cloud alignment on accuracy remain to be thoroughly explored. This work evaluates the errors across the reconstruction pipeline and explores the use of voxel and surface-based accuracy metrics for different segmentation algorithms and geometry types. A sphere, a facemask, and an AAA were printed using the SLA technique and scanned using a micro-CT machine. Segmentation was performed using GMM, Otsu and RG based methods. Segmented and reference models aligned using the KU algorithm, were quantitatively compared to evaluate metrics like Dice and Jaccard scores, precision. Surface meshes were registered with reference meshes using an ICP-based alignment process. Metrics like chamfer distance, and average Hausdorff distance were evaluated. The Otsu method was found to be the most suitable method for all the geometries. AAA yielded low overlap scores due to its small wall thickness and misalignment. The effect of class imbalance on specificity was observed the most for AAA. Surface-based accuracy metrics differed from the voxel-based trends. The RG method performed best for sphere, while GMM and Otsu perform better for AAA. The facemask surface was most error-prone, possibly due to misalignment during the ICP process. Segmentation accuracy is a cumulative sum of errors across different stages of the reconstruction process. High voxel-based accuracy metrics may be misleading in cases of high class imbalance and sensitivity to alignment. The Jaccard index is found to be more stringent than the Dice and more suitable for accuracy assessment for thin-walled structures. Voxel and point cloud alignment should be ensured to make any reliable assessment of the reconstruction pipeline.