A new strategy to achieve large-scale, three-dimensional (3D) micro- and nanostructured surface patterns through selective electrochemical growth on monolayer colloidal crystal (MCC) templates is reported. This method can effectively create large-area (>1 cm2), 3D surface patterns with well-defined structures in a cost-effective and time-saving manner (<30 min). A variety of 3D surface patterns, including semishells, Janus particles, microcups, and mushroom-like clusters, is generated. Most importantly, our method can be used to prepare surface patterns with prescribed compositions, such as metals, metal oxides, organic materials, or composites (e.g., metal/metal oxide, metal/polymer). The 3D surface patterns produced by our method can be valuable in a wide range of applications, such as biosensing, data storage, and plasmonics. In a proof-of-concept study, we investigated, both experimentally and theoretically, the surface-enhanced Raman scattering (SERS) performance of the fabricated silver 3D semishell arrays.