The transport properties of the carbon nanotubes (CNTs) are affected by the tube-tube interaction and the defects presented in the system. Inter-tube bonding, formed during spark plasma sintering (SPS) process, lowers the electrical/thermal resistivity at the tube-tube junctions and also causes new scattering mechanisms such as strong electron-phonon coupling (EPC) at low temperature. More evidences have been found by changing the SPS temperature and doping the CNTs to support the electron-phonon coupling is Kohn anomaly (KA) in as-SPSed CNTs. The phonon drag, appearing in thermoelectric power (TEP) of the as-SPSed CNTs at low temperature, can be explained in the framework of the KA. The thermal property of CNTs exhibits nearly two dimensional character when the inter-tube bonding is stronger. When orientated CNTs are SPSed, one of the highest thermal conductivity ~ 31 W/(m-K) reported in CNT bulk samples is achieved. In certain cases, defects in the CNTs not only change the transport properties but also modify the morphology of the CNTs. Helically coiled carbon nanotubes (HCNTs) and nanowires (HCNWs) are exact examples. A rational synthesis of HCNT/HCNW using In and Sn as catalyst in a thermal chemical vapor deposition (CVD) system has been demonstrated. A thermodynamic model has been proposed, where helix/coil formation is explained on the basis of the interactions between the specific catalyst particles and the growing nanostructure. While a model based on the mutual solubility of Fe with Sn and In, could explain the growth mechanism difference between the HCNTs and the HCNWs. Experimental results agree with these models qualitatively well