We demonstrated holographic vector-wave femtosecond laser processing system based on a holographic manipulation of the light including amplitude, phase and polarization. The system performs a high-throughput and flexible fabrication of orientation-controlled nanostructures applied to material surface modification for control of a tribology, wettability, light reflectance and retardance. In this experiment, a polarization characteristic of the laser processing system was experimentally verified. In addition, parallel fabrication of orientation-controlled nanostructures using multifocal vector beams was performed.