A first working process performs a deposition working or an etching working to a workpiece by face-irradiating a focused ion beam to the workpiece, and a second working process then performs a deposition working or an etching working to the workpiece by edge-irradiating a focused ion beam to an edge of the workpiece. During the first working process, the deposition working or the etching working is performed to add the missing portion or remove the excess portion to a point slightly short of the edge boundary of the workpiece, i.e., to a point that is less than the irradiation width of the focused ion beam. The remaining missing portion or the remaining excess portion is eliminated in the second working process by edge-irradiating the focused ion beam to the edge of the workpiece.