A topographic profile of a structure is generated using atomic force microscopy. The structure is scanned such that an area of interest of the structure is scanned at a higher resolution than portions of the structure outside of the area of interest. An profile of the structure is then generated based on the scan. To correct skew and tilt of the profile, a first feature of the profile is aligned with a first axis of a coordinate system. The profile is then manipulated to align a second feature of the profile with a second axis of the coordinate system.