Carbon nanotubes have remarkable material properties and are ideal for different space applications including thermal management devices, light-weight mechanical shock absorbers, and fiber-reinforced composites. Nanotube junctions, which are the interconnections of carbon nanotubes, have properties different from the pristine structures and are promising materials for constructing unit blocks with excellent material properties. However, widespread application of the junctions and nanostructures is limited due to the lack of understanding of their mechanical, thermal, and electronic properties. The overall objective of the current research is to provide a computational methodology to construct atomistic models of nanostructures and study their thermal and mechanical properties under different operating conditions. In the first part of the research, the topologically accurate atomistic models of the junctions are created using a novel CAD-based remeshing and optimization strategies. The most energetically stable configurations are chosen to build 3D architectures, thus, providing an economical way to construct complex and larger dimension nanostructures. The created macro-structures can be used directly in the atomistic simulations to study their structure-property relationships. In this dissertation, the thermal and mechanical characterization of pristine nanotubes and complex nanotube multiterminal junctions have been studied using molecular dynamics (MD) simulation. At the nanoscale, the thermal conductivity of nanotube is found to be dependent on size, strain, temperature, and defects. The effects of each of these parameters on the thermal transport of nanostructures have been determined using MD. This is followed by the comparative study of the phonon density of states and phonon dispersion relations of different configurations. The study provides guidelines for creating nanotube heat transfer devices with desired thermal specifications. In addition to being highly conductive, nanotubes and junctions have very high strength and modulus. Although an extensive amount of research is available with the characterization of the pristine nanotubes, there lacks a proper understanding of the mechanical characteristics of the complex structures (multi-terminal junctions and micro-blocks). With the atomistic models of these structures created, the tensile and compressive strengths of such complex architectures have been presented. These computational models will provide the much needed next step for the realization of nanotube junctions for the industrial applications.