PROBLEM TO BE SOLVED: To provide a scanning (transmission) electron microscope which enables (a) the three-dimensional (3D) observation of a 0.1 nm-atomic size structure, and (b) the identification of a 3D structure of an atom in a sample, and the material thereof.SOLUTION: The scanning/transmission electron microscope is arranged to enable 3D observation of a 0.1 nm-atomic size structure, and has: an electronic lens system having a small spherical aberration coefficient; an aperture arranged so that an irradiation angle can be changed; an irradiation electronic lens system arranged so that the probe size of an electron beam probe, and the irradiation angle can be changed; a secondary-electron detector; a transmitted electron detector; a forward scattering electron beam detector; a focus controller; an image arithmetic unit for identification of image contrast; an image arithmetic unit for computing for image sharpness; an arithmetic unit for forming a 3D image; and a mixer for mixing secondary electron signals and sample forward scattering electron signals.