This article shows the coarsening behavior of nanoparticle multilayers during heat treatments which produce larger metallic nanostructures with varying shapes and sizes on glass slides. Nanoparticle multilayer films are initially constructed via the layer-by-layer self-assembly of small and monodispersed gold and/or palladium nanoparticles with different compositions (gold only, palladium only, or both gold and palladium) and assembly orders (compounding layers of gold layers over palladium layers or vice versa). Upon heating the slides at $600^{circ}C$, the surface nanoparticles undergo coalescence becoming larger nanostructured metallic films. UV-Vis results show a clear reliance of the layering sequence on the optical properties of these metal films, which demonstrates an importance of the outmost (top) layers in each nanoparticle multilayer films. Topographic surface features show that the heat treatments of nanoparticle multilayer films result in the nucleation of nanoparticles and the formation of metallic cluster structures. The results confirm that different composition and layering sequence of nanoparticle multilayer films clearly affect the coalescence behavior of nanoparticles during heat treatments.