A focused ion beam (FIB) processing system includes a FIB irradiation unit that irradiates a FIB onto a pattern formed in a wafer, to form a section of the pattern, an imaging unit that images the section of the pattern, a calculation unit that calculates a pattern size based on the image of the section, a judgment unit that judges whether or not a differential of the pattern size with respect to time is equal to or below a threshold; and a control unit that stops the FIB irradiation unit if the judgment unit judges that the differential of the pattern size is equal to or below the threshold.