Image deformations caused by electromagnetic interference (EMI) are ones of the most frequent undesirable effects in practical scanning electron microscopy. They usually appear, even although the place chosen for a microscope system fulfills EMI conditions, as periodic deformation of vertical edges of an observed specimen. Available, but still very expensive methods for decreasing their influence are shielding and electromagnetic field compensation. The other approach is digital image processing for its correction. However, elimination of the distortions (with hardware or software methods) would be more effective, when their influence on particular elements of microscope system are known or predictable. Current investigations ascertained in which sections of an electron microscope column the geometric deformations are generated, enabled separation of magnetic field influence on electron beam deflection system and its direct influence on electron beam and finally led to obtain a method for quantitative measurement of magnetic field which penetrates the microscope chamber and the electron gun column. The method uses scanning electron microscope itself and was verified by comparing its results with the ones obtained using alternative magnetic field meter.