Materials science has always been on the forefront of human progress, with a current focus on developing functional materials. These materials are designed to perform sophisticated tasks beyond mere structural applications. This necessitates advanced synthesis strategies that synergistically combine the properties of various constituent phases into high-performance nanocomposite material systems. This thesis explores three distinct physical surface modification methods to develop advanced material systems: dielectric barrier discharge plasma treatment on a mixture of few-layer graphene and cobalt powder, conventional magnetron sputtering on nanoporous carbon cloth, and magnetron sputter inert gas condensation for nanoparticle deposition on silicon substrates. The first method produces a cobalt-graphene nanocomposite with enhanced electrochemical performance, with potential scalability to three-dimensional substrates when employing an additional binder phase. The second method creates a nanocomposite of activated carbon cloth with palladium islands, showcasing successful functionalization of flexible three-dimensional substrates with potential applications as energy materials and sensing. The third approach enhances process control and deposition rates for nanoparticle depositions via magnetron sputter inert gas condensation. Initially, quadrupole mass spectrometry is employed for in situ measurements to advance process control. Subsequently, applying a substrate bias voltage significantly increases the output of nanoparticles from the source, thus incrementally improving this method for future research and applications. To summarize, this thesis presents significant advancements in three physical surface modification methods, highlighting their respective capabilities in functionalizing surfaces and showing pathways towards the functionalization of three-dimensional substrates, marking an important step forward towards the industrial application of advanced high-performance nanocomposite materials.