SrVO3 (SVO) is a complex oxide with interesting optical and conduction properties as an indium-free transparent conducting oxide for electrode applications. In this paper, we report how the surface of SVO can be designed at the nanoscale from self-organized Sr3V2O8 nanostructures (NS) with different shapes and morphologies depending on crystalline orientations. By combining transmission electron microscopy (TEM) and atomic force microscopy (AFM), we compare the characteristics of the NS for SVO films grown on SrTiO3 (STO) polycrystalline substrates, according to combinatorial substrate epitaxy (CSE), with those of NS observed from SVO films deposited on STO single crystalline substrates with different crystallographic orientations ((1 0 0), (1 1 0), (1 1 1)). We are able not only to show that the obtained morphologies are correlated to the specific substrate orientation due to the epitaxial relationships between the NS, the SVO, and the substrate, but also to establish a NS library and determine the necessary crystalline orientations for a certain NS morphology on demand. Finally, dissolution of the NS in water leads to typical inverse imprints on the surface of the film, offering a fast and easy way to pattern the electrodes. This work presents a new way of patterning surfaces with a specific design of self-organized NS.