Plasmonic nanoparticle arrays with a specific lattice arrangement can support surface lattice resonances (SLRs). SLR exhibits a sharp spectral peak and finds many applications including optical sensing and plasmonic lasers. To optimize SLR for application, a robust method that allows the mass production of plasmonic nanoparticle arrays with refined particle morphology and well-defined lattice arrangement is required. In this work, we combine nanosphere lithography (NSL) with thermal annealing or nanosecond-pulsed laser treatment to refine plasmonic nanoparticles in a honeycomb lattice. We comparatively study the effects of the two treatment methods on the particle morphology and lattice arrangement of mono (Ag and Pd) and bi-metallic (Ag-Pd) nanoparticle lattices. In general, thermal annealing preserves the lattice arrangement but fairly changes the particle roundness, while laser treatment produces particles with varying morphologies and spatial distribution. We also theoretically and experimentally investigate the optical responses of Ag nanoparticle lattices produced by different treatment methods. The observed difference in spectra can be attributed to the varying particle morphology, which shifts the localized surface plasmon resonance differently, resulting in a significant change in SLR. These findings provide valuable insights for optimizing plasmonic nanoparticle arrays for various applications.