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This paper presents a low pressure hot embossing method for transferring patterns of vertically aligned carbon nanotubes into thermoplastic substrates. The procedure utilizes the synthesis of carbon nanotubes in discrete patterns on silicon substrates through the vapor liquid solid growth mechanism. The nanotube pattern and silicon stamp is placed on top of a polycarbonate film and locally heated above the glass transition temperature using microwave processing. The weight of the silicon substrate presses the nanotubes into the polycarbonate, resulting in the complete transfer of vertically aligned patterns. The technique is a rapid processing method, which could be used to integrate aligned nanomaterials with MEMS and flexible electronics that are fabricated on a wide range of thermoplastic polymer materials.