Anodic aluminum oxide (AAO) substrates with a self-ordered triangular array of nanopores provide the means to fabricate multiple forms of nano materials, such as nanowires and nanoparticles. This study focuses on nanostructures that emerge in thin films of metals thermally evaporated onto the surface of AAO. Previous work showed that films of different evaporated metals assume dramatically different structures, e.g. an ordered triangular array of nearly monodisperse nanoparticles forms for lead (Pb) while a polycrystalline nanohoneycomb structure forms for silver (Ag). Here, we present investigations of the effects of substrate temperature and deposition angle that reveal the processes controlling the nano particle array formation. Our findings indicate that arrays form provided the grain nucleation density exceeds the pore density and the atomic mobility is high enough to promote grain coalescence. They introduce a method for producing films with anisotropic grain array structure. The results provide insight into the influence of substrate nano-morphology on thin film growth energetics and kinetics that can be harnessed for creating films with other novel nano-structures.