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Quartz is optimum material for micro reactor because of its chemical resistance and high mechanical strength. However, efficient fabrication process of micro-order flow channel on quartz is difficult. We developed nanometer-order depth gradation (3-dimensional) fabrication process for spin-on-glass (SOG) resist using accelerating voltage modulation electron beam (EB) direct writing. After EB exposure, the sample was developed using buffered hydrofluoric acid (BHF). Fabricated pattern depths on SOG were well gradated and the depth resolution was 20 nm per 100 V. Thus, using 3D patterned SOG for ion beam etching mask, fabrication of micro flow channel with 3D gradation on quartz surface is possible. Ion beam etching condition was optimized for fabrication of 3D quartz, and we found out CF4 ion species at 500 V took a high selectivity. Nano-order precise 3D quartz surface was obtained using SOG as an ion beam mask.