An energy filtering system of an EFTEM is automatically adjusted using a computer. The computer inserts an energy-selecting slit into the beam path and begins monitoring the position of the electron beam through a combination of the current sensors integral to the slit and the readout of an electron camera. The beam is centered within the slit by adjusting an energy dispersing element while monitoring beam sensors. After initial alignment, the slit is retracted and a reference aperture is inserted at the entrance to the energy filter. The electron camera captures an image of the reference aperture and the computer analyzes the deviations of the aperture image from its known physical dimensions in order to evaluate the electron optical distortions and aberrations of the filter. The computer uses the determined optical parameters to adjust the distortion and aberration correcting optical elements of the filter, whose effects are known due to previous calibration. After correcting the imaging aberrations, the reference aperture is withdrawn, the slit reinserted, and an isochromatic surface of the filter at the plane of the slit is measured by scanning the beam across a slit edge while integrating the transmitted beam intensity on the electron camera. The isochromatic surface thus collected by the electron camera is analyzed by the computer to extract additional aberration coefficients of the filter system. These measured aberration coefficients are used to make calibrated corrections to the filter optics.