The mechanical properties of nanofiber reinforced polymer microstructures were investigated in this work by means of nanoindentation. The femtosecond laser was used to generate nanofibers on selected area on the surface of the substrate and to generate microstructures. These microstructures were formed via two photon polymerization using femtosecond laser material processing by incorporation of silicon nanofibers into Ormocer matrix. Results show that the hardness and elastic modulus of the nanocomposites have improved by 25% and 75%, respectively, with the incorporation of nanofibers using the described method, which has the potential of direct fabrication of reinforced micro-/nanostructures. The volume fraction of the generated nanofibers in the nanocomposite was calculated by using nanoindentation analysis.