Additive manufacturing, in combination with virtual surgery planning, leads to the predictability of complex surgical cases. To guarantee patient safety, three-dimensional (3D) print quality must be ensured and verified. The aim of this study is to compare the accuracy of an optical white-light desktop scanner (OWLDS) and a cone beam CT (CBCT) scanner to that of a multi-slice CT scanner (MSCT) for scanning and digitizing 3D anatomical models. Twenty-two removable parts of a CE-certified anatomical skull, used as a patient-specific surrogate in a clinical workflow, were each scanned by MSCT, CBCT, and OWLDS scanners. The accuracy of the scanning modalities was investigated through a part comparison analysis of the stereolithography (STL) files derived from the different scanning modalities. The high-resolution OWLDS STL files show the smallest overall surface match deviation, at 0.04 mm, compared to the MSCT STL files. The CBCT STL files show an overall deviation of 0.07 mm compared to the MSCT STL files. This difference between the scan modalities increases as the volume of anatomical models decreases. The OWLDS is a safe, cost-effective, user-friendly, and highly accurate scanning modality suitable for accuracy evaluation during the manufacturing process of in-house 3D models. For smaller models, high-resolution optical scans are recommended.