A method is disclosed for forming an alignment layer for use in a liquid crystal cell layer for use in a liquid crystal cell using an ion beam source that includes the steps of: (1) providing a substrate having a surface; (2) providing an ion beam source that emanates an ion beam; (3) providing a mask layer disposed between the substrate surface and the ion beam source. The mask layer has at least two openings disposed between the ion beam source and the substrate surface. The shape and position of the openings reduce the irregularity of the beam exposure in a border region on the surface of the substrate resulting from the ion beam source. The present invention may be used in conjunction with substrate treatment using multiple sweeps with a single ion beam source, or with a substrate treatment using a single sweep with multiple ion beam sources. Also disclosed is an apparatus for practicing the disclosed method.