We report the surfactant-free vapor-phase synthesis of atomically flat and ultraclean gold nanoplates. These gold nanoplates can offer optimally functional surfaces through the immobilization of molecules without unspecific adsorption and defect, which could be quite valuable for diverse applications including biomedical sensing, plasmonics, molecular electronics, electrochemistry, etc. The ultraflat, ultraclean, and single-crystalline nanostructures, including gold nanoparticles (NPs), gold nanowires (NWs), gold nanobelts, and gold nanoplates, are stereoepitaxially grown on a substrate with a specific orientation. Moreover, the nanostructures can be selectively synthesized by experimental conditions and locations of the substrate. The geometry and orientation of the nanostructures show strong correlations, suggesting a growth process of seed NPs → NWs → nanobelts → nanoplates. This synthetic process can be explained by the mechanism in which the height-to-width ratio of gold nanostructures is determined by the ratio of the atom-supply rate by direct impingement to the atom-supply rate by surface diffusion. We finely tuned the shapes (NPs, NWs, nanobelts, or nanoplates) and sizes (from several micrometers to hundreds of micrometers) of the gold nanostructures by adjusting the deposition flux. Crucially, the surfactant-free and atomically flat gold nanoplates could be optimally bioactive surfaces. We substantially decreased the nonspecific binding of avidin by immobilizing the biotinylated molecules onto the gold nanoplates. Compared with thermally deposited gold films, the single-crystalline gold nanoplates showed a 100 times lower detection limit in the recognition of the biotin-avidin interaction. We anticipate that the gold nanoplates will bring us one-step closer to the realization of ideal biomolecular sensors because the several bioactive gold surfaces can be prepared by immobilizing various biological molecules onto the gold nanoplates.