Teaching internal structures obscured from direct view is a major challenge of anatomy education. High‐fidelity interactive three‐dimensional (3D) micro‐computed tomography (CT) models with virtual dissection present a possible solution. However, their utility for teaching complex internal structures of the human body is unclear. The purpose of this study was to investigate the use of a realistic 3D micro‐CT interactive visualization computer model to teach paranasal sinus anatomy in a laboratory setting during pre‐clinical medical training. Year 1 (n = 79) and Year 2 (n = 59) medical students undertook self‐directed activities focused on paranasal sinus anatomy in one of two laboratories (traditional laboratory and 3D model). All participants completed pre and posttests before and after the laboratory session. Results of regression analyses predicting post‐laboratory knowledge indicate that, when students were inexperienced with the 3D computer technology, use of the model was detrimental to learning for students with greater prior knowledge of the relevant anatomy (P < 0.05). For participants experienced with the 3D computer technology, however, the use of the model was detrimental for students with less prior knowledge of the relevant anatomy (P < 0.001). These results emphasize that several factors need to be considered in the design and effective implementation of such models in the classroom. Under the right conditions, the 3D model is equal to traditional laboratory resources when used as a learning tool. This paper discusses the importance of preparatory training for students and the technical consideration necessary to successfully integrate such models into medical anatomical curricula.