Femtosecond (fs) laser processing is an attractive tool for two-photon polymerization of photosensitive polymer materials. Two-photon absorption leads to precise microfabrication with structural dimensions much smaller than the diffraction limit of the incident laser beam. In addition, polymerization occurs in the localized focal volume, which allows true three-dimensional (3D) microstructuring. This method could be used for the fabrication of new micro/nano-devices. For high speed fabrication, the throughput of fs laser processing must be improved. One of the solutions of this problem is multi-beam processing using beam separation technique. However, for the realization of this technique it is necessary to prepare several sets of optics, shutters, and stage systems for the samples. Furthermore, the multi-focus system based on the beam separation technique does not provide the required task integration for the fabrication of complex structures. To overcome these problems, we demonstrate novel two-photon polymerization multi-focus setup using spatial light modulator. The system consists of femtosecond laser (wavelength: 780nm, pulse width 140fs) and a liquid crystal spatial light modulator (LCSLM). Inorganic/organic hybrid polymers (Ormocers) is used as a sample. The laser is illuminated onto the reflective LCSLM displaying a Computer Generated Holographic (CGH) pattern to modulate the phase of the incident laser beam. The reflected laser beam forms multi-focus spot pattern at the Fourier plane and is projected into the liquid Ormocer sample with a 100x immersion lens microscope objective (NA=1.36). For multi-focus beam nanostructuring, the laser beams are scanned with a computer controlled XYZ axis stage. The multi-focus beams produce several parallel lines with 2.5 um distance from each other. This phase modulated holographic technique can be utilized for multi-focus 3D fabrication and allows to control laser intensity and position for each spot independently.