The perception of 3D features from 2D representations depend on their number of salient features, recognizable canonical axes, and orientations. Informed by form-perception literature, we proposed a hexagonal prism as an external reference frame to identify positions of elements in relation to each other and the observer when studying Diels-Alder and other cycloaddition reactions. The hexagonal prism reference model (HPRM) provides three-dimensional features to cycloaddition transition states and an external reference to facilitate analysis of their stereochemical characteristics. A study to characterize the visual-spatial skills (VSS) and spatial challenges associated with extracting spatial information, representing spatial relations, and predicting stereochemical outcomes was completed with six graduate and six undergraduate students. Our findings show that different VSS predominate when solving different spatial tasks and that the patterns of VSS utilized by both graduate and undergraduates groups can be used to provide a more in-depth subcategorization of spatial strategies. The HPRM not only provides a resource for students to practice VSS and learn cycloaddition stereoselectivity, but also for instructors to promote effective strategies to predict stereochemistry. Since this study did not identify any nonspatial strategy, the HPRM proved to be effective in promoting students' visuospatial thinking to solve spatial tasks.