Carbon nanotubes (CNTs) are among the most promising nanosize materials as evidenced by the attention they have received since their discovery in 1991 and a wide range of scientific and industrial applications. Each of these applications requires unique CNTs with specific length, diameter and chirality. However, control of these parameters is considered as one of the main challenges for large scale production of CNTs. Furthermore, these processes are not well designed so as to limit the number of CNT defect sites or the production of unwanted byproducts such as amorphous carbon. Therefore, it is crucial to develop a controlled CNTs fabrication process that is capable of producing pure CNTs with uniform properties. Along this line of reasoning, a time-dependent multiphysics, multiscale modeling framework is proposed to describe CNTs fabrication using chemical vapor deposition (CVD). The fully integrated model accounts for multiphase chemical reactions as well as fluid, heat and mass transport phenomena. Moreover, the fabrication process is divided into three physical scales. As the first modeling scale, a control volume is placed around the CVD reactor chamber to investigate the effects of physical phenomena on fabrication process effective parameters such as gas phase reaction sets. The obtained information from this scale are then utilized in the substrate scale modeling to investigate these physical effects as well as the effects of substrate dislocation and orientation, on the produced carbon species. Finally, by utilizing molecular dynamics (MD) simulation technique, the diffusivity of carbon species into the deposited nanoparticles and the effects of fabrication temperature on diameter and chirality of CNTs are investigated. The developed model is ultimately utilized to investigate the effect of temperature; total flow rate and feed gases mixture ratio on CNTs growth rate and amorphous carbon formation. As representative outcomes of current research and developed model, CNTs with especial configurations such as Y-shaped, spring-shaped and CNT with variable diameter have been experimentally produced. The outcomes from this study could provide a fundamental understanding and basis for the design of an efficient CNT fabrication process that is capable of producing high yield CNTs and with a minimum amount of amorphous carbon. Moreover, this work can be utilized to introduce a pathway for optimization of a controllable CVD-based CNTs fabrication process when accompanying by some in-situ measurement and diagnosis systems. The optimization process can be selectively tuned depending on the expectation cost and application of CNTs final product criteria.