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This paper investigates the engaging concept of virtual 3D jigsaw puzzles to foster the understanding of spatial relations within technical or biological systems by means of virtual models. Employing an application in anatomy education, it answers the question: How does guided spatial exploration, arising while composing a 3D jigsaw, affect the acquisition of spatial-functional understanding in virtual learning environments (VLE)? In this study, 16 physiotherapy students were interviewed before and immediately after using either a virtual 3D jigsaw puzzle enabled VLE or a simplified version without the interaction specific to the 3D jigsaw concept. Results indicate that students using the jigsaw-enabled VLE achieved a significant better understanding of the spatial and functional correlations illustrated by the model. These findings suggest that the concept of a 3D jigsaw puzzle, with its implicit guidance …