For structures consisting of a thin film bonded to a compliant substrate, wrinkling of the thin film is commonly observed as a result of mechanical instability. Although this surface undulation may be an undesirable feature, the development of new functional devices has begun to take advantage of wrinkled surfaces. The wrinkled structure also serves to improve mechanical resilience of flexible devices by suppressing crack formation upon stretching and bending. If the substrate has a reduced thickness, buckling of the entire structure may also occur. It is important to develop numerical design tools for predicting both wrinkle and buckle formations. In this paper we report a comprehensive finite element-based study utilizing embedded imperfections to directly simulate instabilities. The technique overcomes current computational challenges. The temporal evolution of the wrinkling features including wavelength and amplitude, as well as the critical strains to trigger the surface undulation and overall structural buckling, can all be predicted in a straightforward manner. The effects of model dimensions, substrate thickness, boundary condition, and composite film layers are systematically analyzed. In addition to the separate wrinkling and buckling instabilities developed under their respective geometric conditions, we illustrate that concurrent wrinkling and buckling can actually occur and be directly simulated. The correlation between specimen geometry and instability modes, as well as how the deformation increment size can influence the simulation result, are also discussed.