Two photon polymerization (TPP) lithography has been established as a powerful tool to develop 3D fine structures of polymer materials, opening up a wide range applications such as micro-electromechanical systems (MEMS). TPP lithography is also promising for 3D micro fabrication of nanocomposites embedded with nanomaterials such as metal nanoparticles. Here, we make use of TPP lithography to fabricate 3D micro structural single wall carbon nanotube (SWCNT)/polymer composites. SWCNTs exhibit remarkable mechanical, electrical, thermal and optical properties, which leads to enhance performances of polymers by loading SWCNTs. SWCNTs were uniformly dispersed in an acrylate UV-curable monomer including a few amounts of photo-initiator and photo-sensitizer. A femtosecond pulsed laser emitting at 780 nm was focused onto the resin, resulting in the photo-polymerization of a nanometric volume of the resin through TPP. By scanning the focus spot three dimensionally, arbitrary 3D structures were created. The spatial resolution of the fabrication was sub-micrometer, and SWCNTs were embedded in the sub-micro sized structures. The fabrication technique enables one to fabricate 3D micro structural SWCNT/polymer composites into desired shapes, and thus the technique should open up the further applications of SWCNT/polymer composites such as micro sized photomechanical actuators.