A low-temperature flexible process, named "chemical transfer", was developed to assemble well-aligned carbon nanotube (ACNT) structures onto various substrates. The technology was featured by (1) in situ functionalization of ACNTs with reactive functional groups during the CVD process and (2) covalently bonded interface with a self-assembled monolayer (SAM) of conjugated thiol molecules as the bridging ligand and conduction path at the ACNT/gold interface. The effectiveness of the in situ functionalization was characterized by X-ray photoelectron spectroscopy (XPS) and Fourier transform infrared spectroscopy (FTIR). I-V response and the interfacial strength of the chemically transferred structure were studied. Results showed an Ohmic contact, low electrical resistivity, and improved CNT-substrate adhesion. This novel technique shows promising applications for positioning ACNTs as electrical interconnects or thermal interface materials on temperature-sensitive substrates.