We apply a previously developed asymptotic model (J. Fluid. Mech. 915, A133 (2021)) to study instabilities of free surface films of nanometric thickness on thermally conductive substrates in two and three spatial dimensions. While the specific focus is on metal films exposed to laser heating, the model itself applies to any setup involving films on the nanoscale whose material parameters are temperature-dependent. For the particular case of metal films heated from above, an important aspect is that the considered heating is volumetric, since the absorption length of the applied laser pulse is comparable to the film thickness. In such a setup, absorption of thermal energy and film evolution are closely correlated and must be considered self-consistently. The asymptotic model allows for a significant simplification, which is crucial from both modeling and computational points of view, since it allows for asymptotically correct averaging of the temperature over the film thickness. We find that the properties of the thermally conductive substrate -- in particular its thickness and rate of heat loss -- play a critical role in controlling the film temperature and dynamics. The film evolution is simulated using efficient GPU-based simulations which, when combined with the developed asymptotic model, allow for fully nonlinear time-dependent simulations in large three-dimensional computational domains. In addition to uncovering the role of the substrate and its properties in determining the film evolution, one important finding is that, at least for the considered range of material parameters, strong in-plane thermal diffusion in the film results in negligible spatial variations of temperature, and the film evolution is predominantly influenced by temporal variation of film viscosity and surface tension (dictated by average film temperature), as well as thermal conductivity of the substrate.