The structure of ultrathin silicon oxynitride films, used as gate dielectrics in integrated circuits (ICs), is studied using analytical electron microscopy (AEM). Laterally homogeneous blanket films approximately 2 nm in thickness are characterized in cross section using a 300 keV field emission TEM/STEM. High resolution imaging (HRTEM) is used to investigate the accuracy and precision of film thickness measurements and their comparability to other techniques such as secondary ion mass spectrometry, spectroscopic ellipsometry, x-ray reflectivity, x-ray photoelectron spectroscopy, and medium energy ion scattering. A two dimensional magnification calibration scheme that fits a pair of basis vectors to experimental images is presented, and integrated intensity profiles are used to define film boundaries for measurement. These image processing tools simultaneously improve the repeatability of the measurements and remove subjective operator bias from the measurement process.