The understanding of the lateral morphology stability of thin polymer devices is of fundamental importance. In this work, the lateral morphology in a model system consisting of thin polymer films capped with thin metal layers on a Si substrate is investigated. When the model system is heated above a critical temperature, a characteristic surface topographic structure is observed that has a well-defined periodicity but random orientation. It is shown that the minimum temperature, Tmin, required for the surface pattern to be observed decreases with increasing polymer-film thickness. Increasing either the metal- or polymer-layer thickness increases the characteristic wavelength of the topography. It is believed that the dominating driving force for the surface corrugated-pattern formation is the thermal-expansion-coefficient mismatch of the capping layer and the substrate. A theoretical model based on local bending of a thin, stiff surface film on a thin, elastic medium is used to provide a quantitative analysis of the surface morphology. The calculated minimum temperature required for the surface morphology and the periodicity of the surface patterns to form are in strong agreement with the experimental results. By contrast, systems with prefabricated topographic patterns within any of the three layers (polymer, metal, substrate) produce highly anisotropic surface topographies aligned perpendicular to the prefabricated topographic structure. It is also found that, in a model system with pre-patterned polymer films, a much higher critical temperature is required for the surface morphology to be observed. The changes in apparent stability and morphological orientation in the pre-patterned systems can be understood as a result of the anisotropic release of the lateral surface stress during the heat treatment.