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Submicron orientational patterns were created in thin liquid crystal polymer films. A rubbed polyimide layer was locally modified by hatching it with the small tip of a simplified atomic force microscope. A nematic liquid crystal mixture, that can be spin‐coated and polymerized at room temperature was used to transfer the lithography from the polyimide into the liquid crystal polymer. Gratings as small as 240 nm periods were fabricated. The domain boundaries, which are nothing else than twist disclination lines attached to the substrate surface, influence the topography on a distance much larger than the film thickness. This topographic effect, which consists of a groove and a wall parallel to the boundary, was investigated as a function of the scratching angle, the film thickness and the size of the structure. © 1996 American Institute of Physics.