One of the important venues in designing novel interfaces and materials is based on the complementary functionalization of surfaces, modified molecules, and nanostructures, so that combining them would lead to layers and materials with novel chemical and physical properties. This presentation will focus of the molecular-level view of surface functionalization and extending the molecular approach to nanostructures and nanostructured layers with three-dimensional control. Classical organic reactions will be used to first build a nearly perfect layer of chemically functionalized nanoparticles on a flat surface and then the approach will be extended into the third dimension. The work will combine "click chemistry" with chemical functionalization approach and utilize surface analytical techniques including XPS, infrared spectroscopy, microscopic techniques combined with focused ion beam (FIB) sample preparation and will be complemented with the DFT studies. The spectroscopic techniques combined with DFT modeling will support the chemistry of deposition, while the electron microscopy techniques will confirm the growth of layered structures.