We employed depth-sensing nanoindentation to produce ordered arrays of indents on the surface of 50 nm-thick Au(Fe) films deposited on sapphire substrates. The maximum depth of the indents was approximately one-half of the film thickness. The indented films were annealed at a temperature of 700 °C in a forming gas atmosphere. While the onset of solid-state dewetting was observed in the unperturbed regions of the film, no holes to the substrate were observed in the indented regions. Instead, the film annealing resulted in the formation of hillocks at the indent locations, followed by their dissipation and the formation of shallow depressions nearby after subsequent annealing treatments. This annealing-induced evolution of nanoindents was interpreted in terms of annihilation of dislocation loops generated during indentation, accompanied by the formation of nanopores at the grain boundaries and their subsequent dissolution. The application of the processes uncovered in this work show great potential for the patterning of thin films.