the apertures is correspondingly shaped the travelling direction of the electron beam 2 having a cross section shaped by the apertures 6 and 10 is modified by a deflecting coil 5b to be focused onto an aperture member 12 by an electron lens 11 as a shaped aperture image the marginal portion of the electron beam which is likely to be disturbed is again intercepted off by the aperture member 12 finally the electron beam is projected onto a target 16 in the form of the shaped aperture image the target 16 is constituted by an object to be worked with the shaped electron beam the electron beam is deflected two dimensionally by a deflecting unit 14 so that the target 16 is scanned by the electron beam in accordance with a predetermined pattern a reference numeral 15 denotes a reflected electron detector for detecting electrons reflected from the target 16 with the structure of the electron beam irradiating apparatus of a variable beam section type described above the target 16 is two dimensionally scanned by the electron beam of a rectangular or square cross section shaped by the apertures 6 and 10 under the action of the deflecting coil 14 with the size of the rectangular image being variable by the deflecting plates 8 so as to conform with a pattern to be formed whereby the desired patterns are successively produced as if they were stamped on the target the apparatus for writing a pattern by a beam of charged particles as described above has heretofore been well known according to the present invention the charged particle beam writing system of this type is provided with an axis aligning apparatus for aligning the center axis of the charged particle beam with that of the aperture.