With the development of material science and technology, modification of substrates, which have random geometry and high aspect ratio three dimensional (3D) complex structures, with desired functional, reactive and stable coatings becomes important and challenging. The ability to fabricate mono- or multi-layers of functional materials with precisely controlled dimensions, finely tuned composition and molecular structures, attracts significant interests in materials science and is the key to construct such devices and structures at nano- and micro-scale with desired properties. In this study, supercritical carbon dioxide (scCO₂) has been studied as an alternative route for modifying substrates due to the unique gas-like (low viscosity, high diffusivity and zero surface tension) and liquid-like properties (high density). (1) The reaction kinetics of metal oxides thin film deposition from pyrolysis of metal organics in scCO₂ was studied in detail. This method was demonstrated as a powerful technique to coat oxides, including Al₂O₃, Ga₂O₃ and others, into 3D high aspect ratio complex structure of carbon nanotubes (CNTs) forest. (2) The low temperature scCO ₂ based hydrogenolysis process was developed as a useful way to functionalize aligned CNTs forest with dense Nickel nanoparticles. On the second part of this work, atomic layer deposition (ALD)/molecular layer deposition (MLD), as a vapor phase, stepwise and self-limiting vacuum based deposition process, was demonstrated as a powerful way to form highly conformal and uniform film onto substrates, even into highly complex 3D complex structures. In this study, (4) Metal oxide ALD is applied onto 3D electrospun polymer microfiber mats template to illustrate an effective and robust strategy to fabricate long and uniform metal oxide microtubes with precisely controllable wall thickness. Designer tubes of various sizes and different materials were demonstrated by using this method. (5) By further extending this technique, complex coaxial Al₂O₃/ZnO/Al₂O₃ multilayed microtubular structure is fabricated, which provides an unique platform to study the solid state reaction and diffusion process (Kirkendall Effect) between Al₂ O₃ shells and the confined middle ZnO layers by annealing the samples at 700°C. (6) The extension of ALD-MLD process of polyamides, zinc hybrid, aminosilane self assembly monolayers were studied by various techniques to illustrate the surface reaction mechanism.