The ability to select the way in which atoms and molecules self-organize on a surface is important for synthesizing nanometre scale devices. Here we show how endohedral fullerenes (Er(3)N@C(80)) can be assembled into four distinctive arrangements on a strontium titanate surface template. Each template pattern correlates to a particular reconstruction on n-doped SrTiO(3)(001), made in whole or in part by self-assembled arrays of non-stoichiometric oxide nanostructures. Close-packed assemblies of Er(3)N@C(80) molecules are formed, as well as one-dimensional chains and two-dimensional grids. This method of template-assisted molecular ordering provides a new platform for the development of experimental schemes of classical and quantum information processing at the molecular level.