AFM images are stored in a computer as a three dimensional array of numbers. The array of numbers can be processed, displayed, analyzed and then reported by specialized image processing software. AFM image processing software is typically just a little different than image display software that is used for traditional microscopes, such as optical and scanning electron microscopes. The major difference is that the AFM images have three dimensional topography content and the traditional microscopes do not. ie, traditional microscopes do not have height information.

Definitions for the various function of AFM image processing software are:

Process: Changes the data in the image and includes functions like filtering and background subtraction.

Display: Changes the view of the data on the computer screen and includes the type of colors used and the perspective of the display.

Analysis: Achieves the abstraction of quantitative information such as line roughness.

Report: Images and analysis dialog boxes may be exported to a clipboard or to Microsoft^TM Office products with the report functions.