The rubbing of a polymer layer, a commonly applied process, leads to an anisotropic surface morphology, aligning liquid crystal molecules. Scanning force microscopy can be used to intentionally create areas with a similar anisotropy by operating the instrument at loads in the range of 10(-7) to 10(-5) newtons. These areas have an orientation effect on liquid crystals indistinguishable from the rubbing process, which allows a systematic investigation of the orientation properties of an alignment layer as a function of its nanometer-scale morphology. Refractive index patterns can be tailored with this method by scratching a suitable area, as demonstrated by fabrication of an optical waveguide 6 micrometers wide and 5 millimeters long.