Directed assembly of nanomaterials is a promising route for the synthesis of nanoscale materials. In this paper, we demonstrate the directed-assembly of highly ordered two-dimensional arrays of hierarchical nanostructures with tunable size, spacing and composition. The directed assembly is achieved on lithographically patterned metal films that are subsequently pulse-laser melted; during the brief liquid lifetime, the pattened nanostructures assemble into highly ordered primary and secondary nanoparticles, with sizes below that which was originally patterned. Complementary fluid-dynamics simulations emulate the resultant patterns and show how the competition of capillary forces and liquid metal-solid substrate interaction potential drives the directed assembly. As an example of the enhanced functionality, a full-wave electromagnetic analysis has been performed to identify the nature of the supported plasmonic resonances.