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Focused-ion-beam directly milling strategy was used to fabricate photonic resonators on crystalline silicon-on-insulator substrate. In order to reduce damages such as implanting ions, amorphous layers and re-deposition process which are induced by the ions, a sacrificed silica layer was used as an etching mask and a silicon thermal oxidation process was performed. The transmission spectra of both photonic crystal cavities and micro-ring resonators were measured. The resulting data demonstrate that the Q factors are significantly improved after the oxidation treatment.