Two-dimensional ordered arrays of gold (Au) nanoparticles were fabricated using two different variants of the nanosphere lithography technique. First, ordered arrays of polystyrene nanospheres on Si substrate were used as deposition masks through which gold films were deposited by electron beam evaporation. After the removal of the nanospheres, an array of triangular Au nanodisks was left on the Si substrate. After thermal annealing at increasing temperature, systematic shape transition of the nanostructures from original triangular Au nanodisks to rounded nanoparticles was observed. This approach allows us to systematically vary the size and morphology of the particles. In the second and novel technique, we made use of reactive ion etching to simultaneously reduce the dimension of the masking nanospheres and create arrays of nanopores on the substrate prior to the deposition of the Au films. These samples were subsequently annealed, which resulted in size-tunable and ordered Au nanoparticle arrays with the nanoparticles nested in the nanopores of the templated substrate. With the nanoparticles anchored in the nanopores, the substrate could be useful as a template for growth of other nanomaterials.