A variety of self-assembly patterns, e.g., concentric rings, rods, and pillars, in polymer thin film have been achieved by lithographically induced self-assembly (LISA) in this study. The variations of the LISA patterns are controlled by many operation factors, such as the choice of the polymers, mask topology, process temperatures, surface tension, and so forth. It was found that as the inter- and intramolecular hydrogen bond interactions were incorporated into the polymer [poly(methyl methacrylate-co-methacrylic acid)], novel LISA patterns such as rods and corresponding arrays (concentric ring, triangle, hexagonal, etc.) were formed, in addition to the pillar arrays formed in poly(methyl methacrylate) under the same experimental conditions. The origins of the rod array are determined by the topology of the masks. Under a plain mask, the patterns developed from any nonuniform defects (spots) on the mask or polymer thin film and propagated outward. However, under a mask with protruding flat patterns, the rod patterns started along the edge of the protrusions and propagated inward. By increasing the process temperature, those novel rods and corresponding array patterns could transform back to pillar or pillar arrays.