Films of cylinder-forming polystyrene-block-poly(methyl methacrylate) (bulk intercylinder spacing a(o)) were directed to assemble on surfaces chemically patterned with a hexagonal array of spots (interspot spacing a(s)). The block copolymer domain assembly was investigated as a function of the film thickness and the commensurability between a(o) and a(s). The domains assembled vertically away from and matched the spacing and hexagonal order of the underlying lithographically patterned chemical substrate, provided a, was equal to or up to 6% larger than a(o) and the film thickness was <= 54 rim. In contrast, comparably poor assembly was obtained when a(s) was 8% less than a(o). When a(s) was commensurate with a(o), the cylinder diameter and eccentricity had a lower standard deviation and was more circular, respectively, than that of self-assembled cylinders on a neutral substrate.