An atomic force microscope was used to scribe a polyimide-coated substrate with complex patterns that serve as an alignment template for a nematic liquid crystal. By employing a sufficiently large density of scribe lines, two-dimensional topological defect arrays of arbitrary defect strength were patterned on the substrate. When used as the master surface of a liquid crystal cell, in which the opposing slave surface is treated for planar degenerate alignment, the liquid crystal adopts the pattern's alignment with a disclination line emanating at the defect core on one surface and terminating at the other surface.