Three-dimensional (3D) printed anatomical models are valuable visual aids that are widely used in clinical and academic settings to teach complex anatomy. Procedures for converting human biomedical image datasets, like X-ray computed tomography (CT), to prinTable 3D files were explored, allowing easy reproduction of highly accurate models; however, these largely remain monochrome. While multi-color 3D printing is available in two accessible modalities (binder-jetting and poly-jet/multi-jet systems), studies embracing the viability of these technologies in the production of anatomical teaching models are relatively sparse, especially for sub-structures within a segmentation of homogeneous tissue density. Here, we outline a strategy to manually highlight anatomical subregions of a given structure and multi-color 3D print the resultant models in a cost-effective manner. Readily available high-resolution 3D reconstructed models are accessible to the public in online libraries. From these databases, four representative files (of a femur, lumbar vertebra, scapula, and innominate bone) were selected and digitally color enhanced with one of two strategies (painting or splitting) guided by Feneis and Dauber’s Pocket Atlas of Human Anatomy. Resulting models were created via 3D printing with binder-jet and/or poly-jet machines with important features, such as muscle origin and insertion points, highlighted using multiple colors. The resulting multi-color, physical models are promising teaching tools that will enhance the anatomical learning experience.