Self-assembled films of octadecyltrichlorosilane were patterned with regions of different chemical functionality using extreme ultraviolet interferometric lithography. Unexposed regions of the imaging layers remain terminated in methyl groups, and exposed regions are modified so as to be terminated with polar, oxygen-containing terminal groups. Thin films of symmetric poly(styrene-b-methyl methacrylate) were deposited on the substrates and annealed. Unexposed and exposed regions are preferentially wet by the polystyrene block and poly(methyl methacrylate) block of the copolymer, respectively. The dimensions of the grating patterns on the substrate had periods (L-s) from 1400 to similar to 60 nm. If L-s much greater than L-o (L-o = bulk lamellar period of the block copolymer), then the surface pattern was replicated in the topography of the polymer film with a maximum difference in film thickness of 1/2L(o), on adjacent regions. The topographic pattern of the polymer film was a result of lamellae oriented parallel to the substrate with symmetric wetting on unexposed regions (thickness = nL(o)) and with asymmetric wetting on exposed regions (thickness = (n + 1/2)L-o). As the dimension of L-s approached L-o, the replication of the surface pattern in the topography of the film continued to be observed, but with decreasing difference in thickness over adjacent exposed and unexposed regions. For a surface pattern with L-s approximate to L-o, the lamellae oriented perpendicular to the substrate and were macroscopically aligned with the surface pattern.