A method of determining an applicable threshold for determining the critical dimension of a category of patterns imaged by atomic force scanning electron microscopy is presented. The method includes acquiring, from a plurality of patterns, a pair of images for each pattern; for each pair of images determining a reference critical dimension via an image obtained by a reference instrumentation and determining an empirical threshold applicable to an image obtained by a CD-SEM instrumentation such that the empirical threshold substantially corresponds to the reference critical dimension; determining a threshold applicable to a category of patterns, the threshold being determined from a plurality of empirical thresholds.