The invention is to reduce non-uniformity of a processing shape over a wide range of a single field-of-view.The invention is directed to a method of processing micro electro mechanical systems with a first step and a second step in a processing apparatus including an irradiation unit that irradiates a sample with a charged particle beam, a shape measuring unit that measures a shape of the sample, and a control unit. In the first step, the irradiation unit irradiates a plurality of single field-of-view points with the charged particle beam in a first region of the sample, the shape measuring unit measures the shape of a spot hole formed in the first region of the sample, and the control unit sets, based on measurement results of the shape of the spot hole, a scan condition of the charged particle beam or a forming mask of the charged particle beam at each of the single field-of-view points. In the second step, the irradiation unit irradiates, based on the scan condition or the forming mask set in the first step, a second region of the sample with the charged particle beam.