When a liquid film lies on a nonwettable substrate, the configuration is unstable, and the film spontaneously ruptures to form droplets. This phenomenon, known as dewetting, commonly leads to undesirable morphological changes. Nevertheless, recent works, combining spontaneous dewetting triggered by thermal annealing and topographic pattern-directed dewetting, demonstrate the possibility of harnessing dewetting with a degree of precision on par with that of advanced lithographic processes for high-performance nanophotonic applications. Since resonant behavior is highly sensitive to geometrical changes, predicting quantitatively dewetting dynamics is of high interest. Here, we develop a continuum model that predicts the evolution of a thin film on a patterned substrate, from the initial reflow to the nucleation and growth of holes. We provide an operative framework based on macroscopic measurements to model the intermolecular interactions at the origin of the dewetting process, involving length scales that span from sub-nanometer to micrometer. A comparison of experimental and simulated results shows that the model can accurately predict the final distributions, thereby offering predictive tools to tailor the optical response of dewetted nanostructures.