Thin-film thickness measurements using atomic force microscopy (AFM) comprise two steps: 1. AFM scratching in order to produce an exposed film edge, and 2. subsequent AFM measurement of the corresponding step height across the exposed edge. Although the technique is known, many open questions have limited its wider applications. In order to clarify the open questions, here we first demonstrate how to determine the normal force applied during the scratching in contact mode needed to completely remove films from substrates. In order to determine film thickness from processed AFM images, we discuss two procedures based on the histogram method and polynomial step-function fitting. Mechanisms of the scratching process are elucidated by the analysis of lateral forces and their enhancement during the film peeling. Phase maps of scratched domains recorded in amplitude modulation AFM (tapping) mode display a clear contrast compared to pristine films. Therefore, we suggest their utilization as simple indicators of spatial domains with completely removed films. As an example, here the measurements were done on polymer films fabricated by layer-by-layer deposition of oppositely charged polyelectrolytes composed of poly(allylamine hydrochloride) and poly(sodium 4-styrenesulfonate), while the applicability of the presented method on other materials is discussed in detail.