Quartz resonator is a very important device to generate a clock frequency for information and telecommunication system. Improvement of the productivity of the quartz resonator is always required because huge amounts of resonator are demanded to install to various electronic devices. Resonance frequency of the quartz resonator is determined by the thickness of the quartz crystal wafer. Therefore it is essential to uniform the thickness distribution of the quartz crystal wafer with nanometric level. We propose the improvement process of the thickness distribution of the quartz crystal wafer by numerically controlled correction using atmospheric pressure plasma which is noncontact and chemical removal technique. We have already succeeded in obtaining a thickness uniformity of 33.1nm within 2 min in the thickness correction of an AT-cut quartz crystal wafer with an area of 24 mm × 24 mm. However, increase of removal rate and improvement of correction accuracy are required for industrial manufacturing. Heating effects of the quartz crystal wafer in the removal rate and the correction accuracy were investigated. The heating of the substrate and compensate of the scanning speed of the worktable in accordance with the variation of the surface temperature enabled an increase of 50% in removal rate and 10-nanometric-level accuracy in correction of the thickness distribution of the quartz crystal wafer.