In the last decade, there has been an increased interest on carbon nanotubes (CNTs) for various applications due to their unique structural, electronic, mechanical and chemical properties. Synthesis of CNTs is no more a challenge with the enhancements and diversity in production techniques. The remaining challenges regarding CNTs for high-volume manufacturing and commercial applications are related to the followings; firstly, gaining control over orientation and density of CNTs during growth for building two and/or three dimensional functional structures and secondly, modulating properties of these structures through a facile route. With regards to these challenges, the growth dynamics of vertically aligned carbon nanotubes (VA-CNTs) were investigated in this thesis. The first part of this thesis explains synthesis of VA-CNTs achieved through the use of a newly designed alcohol catalyzed chemical vapor deposition system in detail. Various catalyst layers were used in the experiments for understanding growth mechanism and thereby the effect of synthesis parameters. The catalyst layers were deposited on SiO2 wafers through physical vapor deposition techniques. The configuration of these catalyst layers were engineered to tune the density and alignment of VA-CNTs by considering the competing mechanism between the subsurface diffusion and migration of catalyst particles. In addition, the annealing parameters were investigated for synthesizing taller and aligned CNTs. The characterization of catalyst layers and VA-CNTs were performed using analysis of Scanning Electron Microscopy, Raman Spectroscopy, Atomic Force Microscopy, X-ray Photoelectron Spectroscopy, Electron Energy Loss Spectroscopy, High Resolution Transmission Electron Microscopy and Raman Spectroscopy. In the second part, effect of synthesis parameters such as growth temperature and pressure, carbon source type and concentration were examined to better understand the growth dynamics of VA-CNTs. Physical and structural transitions of CNTs were observed induced by the decomposition reaction processes of various carbon sources at a related growth temperature. Growth behavior of VA-CNTs was investigated under different carbon source concentration and pressure to find an optimum growth range. The results indicated that while the synthesis method followed in this work is a catalytic based process where the reaction kinetics has a profound influence on the growth of VA-CNTs molecular diffusion mechanisms were found to be playing a key role in determining the growth, size, orientation and structural properties of VA-CNTs. Hence, an approach incorporating the kinetic and diffusion related processes were followed for building an empirical model for uncovering the dominant mechanisms responsible for the termination of growth of VA-CNTs. In the following sections of the thesis, the preliminary studies regarding Li intercalation to VA-CNTs and cell growth on CNTs were performed for possible future applications of two and three-dimensional structures based on CNTs. In situ Li intercalation was studied during the growth of VA-CNTs which does not require post processing for the intercalation mechanism as commonly performed in the existing literature. Li intercalation in the CNTs was confirmed by using X-ray Photoelectron Spectroscopy, Electron Energy Loss Spectroscopy and Raman Spectroscopy following the changes induced by the charge transfer from Li to the carbon lattice. In the second application case, used of VA-CNTs were examined as a scaffold for growing mesenchymal stem cells (MSCs). Surfaces covered with VA-CNTs were patterned by using elasto-capillary mechanism to create suitable ‘nests’ for MSCs to be anchored. The cell viability test was conducted on seeded MSCs on CNT nests and indicated no toxic effect of CNT nests when they were used as scaffold. Furthermore, an aging effect of cells on adhesion was investigated. As a conclusion, the work presented here demonstrated that control over structural and surface properties of VA-CNTs could be attained by taking advantage of a wide range of growth parameters such as temperature, pressure and carbon source type. Hence, the two case studies examined in this study demonstrated a path for aligned and denser CNTs synthesized with desired properties using the learnings attained in the first part of the thesis to be used as anode materials for Li ion batteries and as alternative scaffolds for tissue engineering applications.