Epitaxy is a widely used method to grow high-quality crystals. One of the key challenges in the field of inorganic solids is the development of epitaxial single-crystal nanostructures. We describe their formation from block copolymer self-assembly–directed nanoporous templates on single-crystal Si backfilled with Si or NiSi through a laser-induced transient melt process. Depending on thickness, template removal leaves either an array of nanopillars or porous nanostructures behind. For stoichiometric NiSi deposition, the template pores provide confinement, enabling heteroepitaxial growth. Irradiation through a mask provides access to hierarchically structured materials. These results on etchable and non-etchable materials suggest a general strategy for growing epitaxial single-crystal nanostructured thin films for fundamental studies and a wide variety of applications, including energy conversion and storage.