Surface-templated nanostructures on the highly oriented pyrolytic graphite (HOPG) basal plane were created by controlled Cs+- or Ga+-ion bombardment, followed by subsequent oxidation at high temperature, forming molecule corrals. The corrals were then used for template growth of SiOx/Si nanostructures. We demonstrate here that, for SiOx/Si nanostructures formed in controlled molecule corrals, the amount of silicon deposited on the surface is directly correlated with the corral density, making it possible to generate patterned SiOx/Si nanostructures on HOPG. Since the size, depth, position, and surface density of the nanostructures can be controlled on the HOPG, it is possible to produce surfaces with patterned or gradient functionalities for applications in fields such as biosensors, microelectronics, and biomaterials (e.g., neuron pathfinding). If desired, the SiOx structures can be reduced in size by etching in dilute HF, and further oxidation of the nanostructures is slow enough to provide plenty of time to functionalize them using ambient and solution reactions and to perform surface analysis. Organosilane monolayers on surface-templated SiOx/Si nanostructures were examined by X-ray photoelectron spectroscopy, time-of-flight secondary ion mas spectrometry, and atomic force microscopy. Silanes with long alkyl chains such as n-octadecyltrichlorosilane (C-18) were found to both react on SiOx/Si nanostructures and to condense on the HOPG basal plane. Shorter-chain silanes, such as 11-bromoundicyltrimethoxysilane (C-11) and 3-mercaptopropyltrimethoxysilane (C-3) were found to react preferentially with SiOx/Si nanostructures, not HOPG. The SiOx/Si nanostructures were also found to be stable toward multiple chemical reactions. Selective modification of SiOx/Si nanostructures on the HOPG basal plane is thus achievable.