A method of optimizing a computer-generated hologram based on parallel second harmonic generation is proposed for holographic femtosecond laser processing. The method, which we call second harmonic optimization, incorporates the width and spatial profile of the pulse into the hologram design. With this method, we demonstrated parallel laser processing with high quality. Because of the enhanced processing accuracy, smaller structures were processed with a smaller energy than in our previous work. In parallel laser processing with 18 beams on a glass surface, the minimum average diameter of the processed structures was 271 nm when the mean fluence of the beams was 0.88 J/cm(2).