This letter reports a versatile nonlithographic technique for mass fabricating three types of technologically important materials-polymer microwell arrays, 2D-ordered magnetic nanodots, and semiconductor nanopillar arrays, each with high crystalline qualities and wafer-scale sizes. Spin-coated hexagonal non-close-packed silica colloidal crystals embedded in a polymer matrix are used as starting templates to create 2D polymeric microwell arrays. These through-hole arrays can then be used as second-generation templates to make periodic magnetic nanodots and semiconductor nanopillars. This self-assembly approach is compatible with standard semiconductor microfabrication, and complex micropatterns can be created for potential device applications. The wafer-scale technique may find important applications in biomicroanalysis, high-density magnetic recording media, and microphotonics.