A method for direct in situ thickness measurements of ultra-thin soft polymer films is presented in which an atomic force microscope (AFM) tip is used to create a furrow in the film, whereby the thickness is determined by scanning the sample across the furrow with the AFM. The sample does not need to be moved since the scratching and the measurements are performed with the same apparatus. This `furrow method' is applied to layer-by-layer polymer/polyelectrolyte ultra-thin films onto hydrophilic glass and silicon wafer substrates. This procedure is made possible because the polymeric film is less stiff than the substrates and the silicon tip. Results for 10-12-bilayer films are comparable to those obtained from profilometry, whose accuracy is only reasonable for films with more than ten bilayers. Taken together, the AFM and profilometer results show that film thickness increases linearly with the number of bilayers. Furthermore, the film thickness does not seem to depend on the substrate used but only on the number of bilayers deposited.