Three-dimensional (3D) hierarchical wrinkles can be generated on prestrained thermoplastic substrates by sequential cycles of skin layer growth followed by the release of prestrain. However, no mechanics models have explained the formation of multigenerational nanostructures using this nanofabrication process. This article describes an analytical model that can represent multiscale wrinkles with arbitrary numbers of generations. Structural features including wrinkle wavelengths and amplitudes on the nanoscale that are predicted by minimizing the total deformation energy of the system. The calculated wavelengths in each generation are in good agreement with experiment. Our mathematical approach provides design principles for achieving multigenerational hierarchical structures.