We present results demonstrating directed self-assembly of nanometer-scale mounds during molecular beam epitaxial growth on patterned GaAs (001) surfaces. The mound arrangement is tunable via the growth temperature, with an inverse spacing or spatial frequency which can exceed that of the features of the template. We find that the range of film thickness over which particular mound arrangements persist is finite, due to an evolution of the shape of the mounds which causes their growth to self-limit. A difference in the film thickness at which mounds at different sites self-limit provides a means by which different arrangements can be produced.