The morphology of sphere-forming block copolymers assembled in thin films on patterned surfaces is theoretically analyzed. The patterns on the lower surface are alternating bands of a given width distinctively attracting or repelling a given block. We find that long-range order can be achieved, and it depends On the commensurability of the characteristic length of the block domains with both band periodicity and slit thickness. The comparison of the simulation results with experimental data shows a very good agreement. Furthermore, we show that the proper selection of the band periodicity and, consequently, of the film thickness permits the system to switch from hexagonal packing to body-centered orthohedra. Therefore, we show that it exists a way to control the formation of long-range ordered structures of different types in this kind of system.