Self-assembled films of octadecyltrichlorosilane (OTS) on Si/SiO2 were patterned with proximity X-rays (lambda = 1.0 nm) in air, resulting in the incorporation of oxygen-containing functional groups, that is, hydroxyl and aldehyde, into the film. Unexposed and exposed OTS exhibited sufficient chemical contrast for patterning processes based on differences in wetting behavior and chemical reactivity. Latent images of features as small as similar to 70 nm, defined by the X-ray mask, were successfully fabricated in the OTS with high fidelity over areas of similar to1 cm(2). Patterned OTS was imaged directly with lateral force microscopy and indirectly through atomic force microscopy of three-dimensional structures formed on the surface of thin films of diblock copolymers after deposition and annealing on the patterned OTS. Pattern transfer of features with dimensions as small as similar to 150 nm into the underlying silicon substrate was achieved by reactive ion etching using thin films of nickel selectively deposited onto the exposed areas of the OTS as etch masks.