3D printing represents an emerging technology with significant potential to advance life-science education by allowing students to directly explore the relationship between macromolecular structure and function. In this article and supplemental video guide, we describe our development of a model-based instructional module on DNA supercoiling and outline practical tips for implementing models in undergraduate classrooms. We also present a procedure to design and print 3D dynamic models for classroom use. Furthermore, we describe repositories of 3D biomolecule files to make using models accessible and cost-effective.