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 a huge amount of the resonator is demanded for installing to various electronic devices. Resonance frequency of the quartz resonator is decided by the thickness of the quartz crystal wafer. Therefore, it is necessary to uniform the thickness distribution of the wafer with nanometric level. We have proposed the improvement technique of the thickness distribution of the quartz crystal wafer by numerically controlled correction using atmospheric pressure plasma which is non-contact and chemical removal technique. Heating effects of the quartz 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 according to the variation of the surface temperature enabled an increase of 50% in the etching rate and 10-nanometric-level accuracy in the correction of the thickness distribution of the quartz wafer, respectively.