In this work, we demonstrate the use of laser-induced periodic surface structures (LIPSS) as templates for the selective growth of ordered micro- and nanostructures of ZnO. Different types of LIPSS were first produced in Si-(100) substrates including ablative low-frequency spatial (LSF) LIPSS, amorphous-crystalline (a–c) LIPSS, and black silicon structures. These laser-structured substrates were subsequently used for depositing ZnO using the vapor–solid (VS) method in order to analyze the formation of organized ZnO structures. We used scanning electron microscopy and micro-Raman spectroscopy to assess the morphological and structural characteristics of the ZnO micro/nano-assemblies obtained and to identify the characteristics of the laser-structured substrates inducing the preferential deposition of ZnO. The formation of aligned assemblies of micro- and nanocrystals of ZnO was successfully achieved on LSF-LIPSS and a–c LIPSS. These results point toward a feasible route for generating well aligned assemblies of semiconductor micro- and nanostructures of good quality by the VS method on substrates, where the effect of lattice mismatch is reduced by laser-induced local disorder and likely by a small increase of surface roughness.