We present a new fast atom beam (FAB) processing method called the moving mask FAB (MM-FAB) processing method that uses relative motion between a patterned separated mask and a workpiece to fabricate multiple microstructures. To evaluate the performance of this method, we developed a micro-positioner to control the relative motion between the patterned separated mask and the workpiece and applied the micro-positioner to fabricate micro-optics arrays, which are multiple microstructures. The separated mask was a 10 mu m thick nickel film with micrometer-sized multiple patterned holes. This mask had been made by electroforming. The workpiece was either glass or GaAs. The FAB source had parallel-plate electrodes and used either SF6 (sulfur hexafluoride) gas (for the glass workpiece) or Cl-2 (chlorine) gas (for GaAs). The mask and the workpiece were moved relative to each other by the developed micro-positioner. We demonstrated the fabrication of a micro-diffraction grating-like object whose height is 230 nm, pitch is 40 mu m by GaAs, and we confirmed that the etching depth is in proportion to the FAB exposure time. Our success in fabricating the micro-optics arrays demonstrated that the combination of FAB processing and relative motion between a mask and a workpiece is effective for producing multiple microstructures that have sloped or curved surfaces.