Scanning transmission electron microscopy (STEM) imaging is applied to analyze the electromigration-induced thickness variations of thin polycrystalline films, It is shown that a high angle annular dark field (HAADF) detector is required to minimize the effect of diffraction contact. A further reduction of the diffraction contrast can be obtained using a tilt series. A correlation between the intensity of the STEM signal obtained with the HAADF detector and the real thickness value was found by comparing corresponding STEM and AFM images. STEM in combination with a tilt series can determine the material distribution in polycrystalline films and can accurately analyze 1-3 nm gaps of nanoelectrodes formed by electromigration.