Mastering the many different diagrammatic representations of molecules used in organic chemistry is challenging for students. This article summarizes recent research showing that manipulating 3-D molecular models can facilitate the understanding and use of these representations. Results indicate that students are more successful in translating between diagrams when they have models available, that using a model to enact the translation process in the world is predictive of learning, and that using models as feedback (to check the accuracy of diagram translation) is particularly effective. Model-based feedback is superior to verbal feedback alone, models scaffold learning rather than act as a crutch, learning with model-based instruction is resilient over a delay of several days, and learning with models transfers to performance when models are no longer available. Finally, virtual models are equivalent to hand-held models in promoting learning in the studied contexts.