A strong understanding of molecular structure is key for mastering structure-function concepts in life sciences and is based on the visualization of biomolecules. Therefore, various approaches to help students translate between the 2D space of a textbook figure to the 3D space of a molecule have been developed. Object-based learning is an approach that gives students a tangible way to view and manipulate physical structures in three dimensions, strengthening learning and challenging students to engage with and interrogate the object. In this work, atomically accurate physical models of macromolecules have been fabricated using consumer-grade 3D printers and integrated into two lectures. The impact of the models on students' ability to overcome common misunderstandings related to proteins and DNA structures was evaluated in a randomized controlled experiment using a compensatory research design. To our knowledge, this is the first time when such a design, where each of the two groups of students works alternatively as a control and as an intervention group, has been used to evaluate the impact of physical models on learning gains. Presenting the physical molecular models in the class and allowing students 3-5 min to handle them was enough to convert low-gain lectures into medium-gain lectures. The students found the models helpful because they offered a hands-on experience, enhancing their focus and engaging their visual memory. Despite some identified drawbacks, using physical models of molecules fabricated using 3D printing is a great way of improving bio-molecular education with low costs.