We have observed that a featureless polymer thin film on a flat plate that is separated from another flat plate by a liquid filled gap can self-assemble into a periodic micropillar array. Moreover, we have observed that if there is a pattern on one of the plates, the boundary of the pillar array will align with the boundary of the pattern resulting in single domain arrays. The phenomenon is believed to be due to the unstable growth of surface waves in the polymer system caused by an attractive Coulombic interaction between the top plate and polymer. A transition temperature has been found below which ordered patterns are not observed in the bilayer system. This self-assembled phenomenon suggests a novel way of controlling flow in microfluidic devices.