Rodent enamel microstructure has been extensively investigated, primarily on the basis of 2D electronic microscopy data. The nature and dynamics of the ameloblasts (the enamel-secreting cells) have also been well studied. However, critical issues still remain surrounding exactly how the ameloblasts produce the astonishing microstructural complexity of enamel, and how this subtle architecture evolved through time. In this article, we used a new methodology based on confocal laser microscopy to reconstruct the enamel microstructure of rodent incisors in three dimensions (3D) with the ameloblasts in situ. We proposed interpretations regarding the possible relationships between the workings of the ameloblasts and the resulting enamel prisms, especially how the phenomenon of decussation is generated. Finally, we were able to represent the two main types of modern rodent incisor microstructures (uniserial and multiserial decussations), as a set of parameters that have been entered into the 3D enamel simulation software Simulenam to generate 3D models that can be digitally manipulated. Associating 2D data of incisor enamel microstructure of fossil rodents and Simulenam, it was then possible to better understand how the various decussation parameters evolved through time and gave rise to the two modern microstructure types from the same ancestral type (pauciserial). This study also confirmed that rodent and artiodactyl enamel do not share the same mechanism of decussation formation.