A nano-stereolithography is the direct patterning process with a nanoscale resolution using twophoton absorption induced by a femtosecond laser. However, in the majority of the works, the fabrication of 3D microstructures have been done only onto transparent glass due to the use of an oil immersion objective lens for achieving a high resolution. In this work, the coaxial illumination and the auto-focusing system are proposed for the direct patterning of nano-precision patterns on an opaque substrate such as a silicon wafer and a metal substrate. Through this work, 3D polymer structures and metallic patterns are fabricated on a silicon wafer using the developed process.