A novel technique based on backscattered electrons (BEs) for accurate determination of thickness (Z metrology) of thin metal films with electron-beam (e-beam) machines is presented. The algorithm, based on phenomenological considerations accounting for the basic electron-material interactions in both the sample and the substrate, results in a relationship between the electron detector counts and the actual height of the samples, having the shape of a saturating exponential of the type 1-e(-(h/ho)), and identifies the associated uncertainties. The algorithm has been tested on Au electroplated features on bulk Si substrates, having thicknesses ranging from 50 to 480 nm, previously measured with conventional techniques such as profilometry and scanning electron microscopy. The e-beam system used in this study is a lithography machine used in metrology mode at 40 kV, a Leica EBMF 10 cs/120, by which BEs were collected through its standard channel plate electron detector, The e-beam scan results are transformed into thicknesses’ measurements by means of the proposed algorithm. Au features were also tested on 100-nm-thick silicon nitride membranes? and the feasibility of the algorithm was pointed out. Achievable errors for both Si bulk and silicon nitride membrane substrates range from about 30% for thin markers to about 10% for thicker ones, making it possible, for thick samples, to exploit the algorithm for measuring thicknesses of phase-working devices.