As the integration scale of transistors/devices in a chip/system keeps increasing, effective cooling has become more and more important in microelectronics. To address the thermal dissipation issue, one important solution is to develop thermal interface materials with higher performance. Carbon nanotubes, given their high intrinsic thermal and mechanical properties, and their high thermal and chemical stabilities, have received extensive attention from both academia and industry as a candidate for high-performance thermal interface materials. The thesis is devoted to addressing some challenges related to the potential application of carbon nanotubes as thermal interface materials in microelectronics. These challenges include: 1) controlled synthesis of vertically aligned carbon nanotubes on various bulk substrates via chemical vapor deposition and the fundamental understanding involved; 2) development of a scalable annealing process to improve the intrinsic properties of synthesized carbon nanotubes; 3) development of a state-of-art assembling process to effectively implement high-quality vertically aligned carbon nanotubes into a flip-chip assembly; 4) a reliable thermal measurement of intrinsic thermal transport property of vertically aligned carbon nanotube films; 5) improvement of interfacial thermal transport between carbon nanotubes and other materials. The major achievements are summarized. 1. Based on the fundamental understanding of catalytic chemical vapor deposition processes and the growth mechanism of carbon nanotube, fast synthesis of high-quality vertically aligned carbon nanotubes on various bulk substrates (e.g., copper, quartz, silicon, aluminum oxide, etc.) has been successfully achieved. The synthesis of vertically aligned carbon nanotubes on the bulk copper substrate by the thermal chemical vapor deposition process has set a world record. In order to functionalize the synthesized carbon nanotubes while maintaining their good vertical alignment, an in situ functionalization process has for the first time been demonstrated. The in situ functionalization renders the vertically aligned carbon nanotubes a proper chemical reactivity for forming chemical bonding with other substrate materials such as gold and silicon. 2. An ultrafast microwave annealing process has been developed to reduce the defect density in vertically aligned carbon nanotubes. Raman and thermogravimetric analyses have shown a distinct defect reduction in the CNTs annealed in microwave for 3 min. Fibers spun from the as-annealed CNTs, in comparison with those from the pristine CNTs, show increases of ~35% and ~65%, respectively, in tensile strength (~0.8 GPa) and modulus (~90 GPa) during tensile testing; an ~20% improvement in electrical conductivity (~80000 S m⁻¹) was also reported. The mechanism of the microwave response of CNTs was discussed. Such an microwave annealing process has been extended to the preparation of reduced graphene oxide. 3. Based on the fundamental understanding of interfacial thermal transport and surface chemistry of metals and carbon nanotubes, two major transfer/assembling processes have been developed: molecular bonding and metal bonding. Effective improvement of the interfacial thermal transport has been achieved by the interfacial bonding. 4. The thermal diffusivity of vertically aligned carbon nanotube (VACNT, multi-walled) films was measured by a laser flash technique, and shown to be ~30 mm² s⁻¹ along the tube-alignment direction. The calculated thermal conductivities of the VACNT film and the individual CNTs are ~27 and ~540 W m⁻¹ K⁻¹, respectively. The technique was verified to be reliable although a proper sampling procedure is critical. A systematic parametric study of the effects of defects, buckling, tip-to-tip contacts, packing density, and tube-tube interaction on the thermal diffusivity was carried out. Defects and buckling decreased the thermal diffusivity dramatically. An increased packing density was beneficial in increasing the collective thermal conductivity of the VACNT film; however, the increased tube-tube interaction in dense VACNT films decreased the thermal conductivity of the individual CNTs. The tip-to-tip contact resistance was shown to be ~1×10⁻⁷ m² K W⁻¹. The study will shed light on the potential application of VACNTs as thermal interface materials in microelectronic packaging. 5. A combined process of in situ functionalization and microwave curing has been developed to effective enhance the interface between carbon nanotubes and the epoxy matrix. Effective medium theory has been used to analyze the interfacial thermal resistance between carbon nanotubes and polymer matrix, and that between graphite nanoplatlets and polymer matrix.