A femtosecond laser processing system with a spatial light modulator (SLM) and its application are presented. Three-dimensional refractive index structures can be fabricated inside glasses by focusing femtosecond laser pulses. When a three-dimensional structure is created, number of processing time is necessary. In addition, fast scanning cannot be applied to shorten the processing time, because long exposure time of laser pulses is necessary to avoid a formation of cracks in the photoexcited region. Therefore, fabrication efficiency is a critical problem. Our laser processing system with an SLM can improve the fabrication efficiency, because multiple light spots can be generated by modulating the spatial phase distribution of laser beam with an SLM. In this paper, we will present the principle of the laser machining system as well as the applications for parallel writing of 3D optical waveguides, diffractive gratings, and optical data storage.