With scaling down the size of the features in modern electronic devices, it becomes vital to control surface reactions at the interface for clean deposition on semiconductor substrates. Chemical functionalization of silicon surfaces provides a new approach for tuning the structure and properties of the interfaces formed with this semiconductor. The functionalized surfaces, such as H− Si(100), NH−Si(100), and NH 2 −Si(100) can be used to prevent surface oxidation at the silicon interface, and OH−Si(100) can be utilized to limit surface diffusion in a reaction with a metal−organic precursor. A model copper metal−organic precursor, copper (hexafluoroacetylacetonato)vinyltrimethylsilane or Cu(hfac)-VTMS, was used to grow copper nanostructures by chemical vapor deposition (CVD), as verified by atomic force microscopy (AFM), infrared spectroscopy (MIR-FTIR), X-ray photoelectron spectroscopy (XPS), and temperatureprogrammed desorption (TPD) supported with density functional theory calculations (DFT). These methods help to follow surface reaction products and kinetics of surface processes. The NH 2 −Si(100) surface yields the largest copper nanostructures at room temperature, and this surface is the most reactive in the CVD process. Understanding the molecular-level mechanisms of the copper deposition onto functionalized surfaces will help to control the nanostructure formation, their properties, and the interface with the solid substrate.