Atomic force microscopy scanning and image processing

A method for generating a topographic profile of a structure, the method comprising:

• scanning the structure, wherein an area of interest of the structure is scanned at a higher resolution than portions of the structure outside of the area of interest, wherein scanning the structure comprises:
• scanning the portions outside the area of interest at a first scan speed;
• and
• scanning the area of interest at a second scan speed slower than the first scan speed;
• generating a profile of the structure based on the scan;
• aligning a first feature of the profile with a first axis of a first coordinate system;
• and
• manipulating the profile to align a second feature of the profile with a second axis of the first coordinate system.