The stability of thin poly(methyl-methacrylate) (PMMA) films of low molecular weight on a solid substrate is controlled by the areal coverage of gold nanoparticles (NPs) present at the air-polymer interface. As the polymer becomes liquid the Au NPs are free to diffuse, coalesce, and aggregate while the polymer film can change its morphology through viscous flow. These processes lead at the same time to the formation of a fractal network of Au NPs and to the development of spinodal instabilities of the free surface of the polymer films. For thinner films a single wavelength is observed, while for thicker films two wavelengths compete. With continued heating the aggregation process results in a decrease in coverage, the networks evolve into disordered particle assemblies, while the polymer films flatten again. The disordering occurs first on the smallest scales and coincides (in thicker films) with the disappearance of the smaller wavelength. The subsequent disordering on larger scales causes the films to flatten.