This paper reports a simple colloidal templating technology for fabricating periodic binary nanostructures, including intercalated arrays of silica spheres and polymer posts, gold nanohole arrays with binary sizes, and biomemetic dimple-nipple antireflection coatings, which are not easily available by traditional top-down and bottom-up approaches. Double-layer, nonclose-packed colloidal crystals prepared by a spin-coating technology are used as etching masks to define the resulting binary crystalline structures. Contrary to conventional colloidal lithography, the polymer matrix between the self-assembled colloidal crystal has also been utilized as a sacrificial template. This bottom-up technique is compatible with standard top-down microfabrication, enabling scalable production of periodic binary nanostructures that have important technological applications ranging from plasmonic devices to broadband antireflection coatings for flat panel displays and efficient solar cells.