Massively parallel femtosecond laser processing with more than 1000 beams was demonstrated. Parallel beams were generated by a computer-generated hologram (CGH) displayed on a spatial light modulator (SLM). The key to this technique is to optimize the CGH in the laser processing system using a scheme called in-system optimization. It was analytically demonstrated that the number of beams is determined by the horizontal number of pixels in the SLM NSLM that is imaged at the pupil plane of an objective lens and a distance parameter pd obtained by dividing the distance between adjacent beams by the diffraction-limited beam diameter. A performance limitation of parallel laser processing in our system was estimated at NSLM of 250 and pd of 7.0. Based on these parameters, the maximum number of beams in a hexagonal close-packed structure was calculated to be 1189 by using an analytical equation.