In this research, we have focused on the morphological evolution of a model metal film / silicon substrate system. When aluminum (Al) is physical vapor deposited on (100) oriented single crystal silicon (Si) at 280 °C it grows heteroepitaxially. Crystallographically, the resulting films are a Potts model system with degeneracy two; their topology simulates a polycrystalline grain structure, with the two types of grains enveloping each other in a convoluted, maze-like arrangement. The morphological evolution of the films during annealing was determined via a combination of transmission electron microscopy (TEM) and atomic force microscopy (AFM). Films with thickness' of 100 to 500 nm were annealed in-situ in the TEM from 250 °C to 550 °C, and characterized using a (220) two-beam condition from one of the grain orientations. This yields predominantly white on black images, which are amenable to quantitative image processing techniques. As anticipated, the grain size increased linearly during the first annealing cycle. Also so-called sub-grain boundaries were observed. These low angle boundaries originate during film deposition when arrays of dislocations are introduced in the areas where coalescing islands of the same orientation meet. After cooling and reheating the sub-grain boundaries disappear. This happens because upon cooling, misfit dislocations were introduced into the films to relieve the thermal misfit strain, resulting in a dense array of dislocations at the film / substrate interface. These thermal misfit dislocations interact strongly with pre-existing sub-grain dislocations; this, in effect, heals the microstructure.