Cylinder-forming poly(styrene-b-methyl methacrylate) (PS-b-PMMA) thin films were directed to assemble on chemically nanopatterned surfaces consisting of alternating stripes that were preferentially wet by the two blocks of the copolymer. The cylindrical domains oriented in the plane of the film and formed defect-free periodic arrays over large areas in registration with the underlying chemical surface pattern if three constraints were satisfied: the substrate pattern period (L-S) was commensurate with the bulk intercylinder period of the block copolymer (L-O), the initial film thickness was quantized with respect to the thickness of a half layer (L/2) or single layer of cylinders (L), and the widths of adjacent stripes of the chemical surface pattern were nearly equal.