The electron-microscope image distortion generated by electromagnetic interference (EMI) is an important problem for accurate imaging in scanning electron microscopy (SEM). Available commercial solutions to this problem utilize sophisticated hardware for EMI detection and compensation. Their efficiency depends on the complexity of distortions influence on SEM system. Selection of a proper method for reduction of the distortions is crucial. The current investigations allowed for a separation of the distortions impact on several components of SEM system. A sum of signals from distortion sources causes wavy deformations of specimen shapes in SEM images. The separation of various reasons of the distortion is based on measurements of the periodic deformations of the images for different electron beam energies and working distances between the microscope final aperture and the specimen. Using the SEM images, a direct influence of alternating magnetic field on the electron beam was distinguished. Distortions of electric signals in the scanning block of SEM were also separated. The presented method separates the direct magnetic field influence on the electron beam below the SEM final aperture (in the chamber) from its influence above this aperture (in the electron column). It also allows for the measurement of magnetic field present inside the SEM chamber. The current investigations gave practical guidelines for selecting the most efficient solution for reduction of the distortions.