Embodiments disclosed herein relate generally to methods for measuring a characteristic of a substrate. In an embodiment, the method includes scanning over the substrate with a scanning probe microscope, the substrate having fins thereon, the scanning obtaining images showing respective fin top regions of the fins, the scanning probe microscope interacting with respective portions of sidewalls of the fins by a scanning probe oscillated during the scanning, selecting images obtained at a predetermined depth below the fin top regions to obtain a line edge profile of the fins, by a processor-based system, analyzing the line edge profile of the fins using power spectral density (PSD) method to obtain spatial frequency data of the line edge profile of the fins, and by the processor-based system, calculating line edge roughness of the fins based on the spatial frequency data.