We investigated a simple and low-cost route for the formation of metallic nanodots on Si substrates ordered in size and position and laterally isolated by SiO2. The method was based on a two-step process: (i) the formation of a nanopattern of ordered cylindrical pores on oxidized Si substrates through self-assembly of diblock copolymers, and successive oxide dry etching down to the Si; (ii) the deposition of gold nanodots and thermal diffusion over the nanopatterned oxide substrates. After diffusion, the nanodot density outside the nanopores was found to decrease, and most of the nanodots were found to saturate the nanopores. The process was followed in situ by transmission electron microscopy (TEM) and ex situ by scanning electron microscopy (SEM) analysis for different thermal budgets. This patterned substrate can be used for catalyst mediated growth, for example, through vapor-liquid-solid (VLS), of nanowires for the formation of absorber materials in novel photovoltaic architectures.