Three-dimensional (3D) modeling is a recent, innovative approach to teaching anatomy. There is little literature, however, to suggest how 3D modeling is best used to teach students and whether or not students can gain the same level of understanding as they might use more traditional, hands-on, teaching methods. This study evaluated the use of a 3D modeling software in both a flipped classroom curriculum and as an active learning tool in comparison to traditional, physical model-based teaching. Pre- and post-course content-based assessments were used to evaluate students' learning. Our findings indicated no significant difference between standard and flipped classroom learning; however, the students who used 3D modeling software as an active learning tool significantly underperformed students in the standard group (F(2,1060) = 112.43, p < 0.0001). These findings suggest that these technologies may not yet be useful as a primary means of instruction. Possible explanations may include cognitive overload in navigating the system, intrinsic limitations of the software, or other factors. Further development and research of these technologies is necessary prior to their adoption into teaching practices in anatomy.