Large-scale fabrication of periodic nanostructures with resolution beyond optical diffraction limitation is of great technological importance in developing next-generation electronic, optical, magnetic, and bio-analytical devices. Bottom-up self-assembly and templating nanofabrication provide a much simpler, faster, and inexpensive alternative to top-down nanolithography (e.g., electron-beam lithography, focused ion beam, and nanoimprint lithography) in creating periodic nanofeatures. Unfortunately, this bottom-up approach suffers from low throughput and incompatibility with mature microfabrication, limiting the mass-production and on-chip integration of practical devices. Here we report a spin-coating technique that combines the simplicity and cost benefits of bottom-up self-assembly with the scalability and compatibility of standard top-down nanofabrication. Spin-coating enables wafer-scale production of colloidal crystals consisting of sub-100 nm particles. A large variety of functional periodic nanostructures ranging from self-cleaning antireflection coatings and magnetic nanodots to reproducible surface-enhanced Raman scattering (SERS) substrates and plasmonic nanohole arrays have also been templated from the shear-aligned nanoparticle arrays. The optical and SERS properties of the templated nanosystems have been characterized by both experimental measurement and theoretical simulation.