It's interesting to compare AFM and its precursor -- Scanning Tunneling Microscope. In some cases, the resolution of STM is better than AFM because of the exponential dependence of the tunneling current on distance. The force-distance dependence in AFM is much more complex when characteristics such as tip shape and contact force are considered. STM is generally applicable only to conducting samples while AFM is applied to both conductors and insulators. In terms of versatility, needless to say, the AFM wins. Furthermore, the AFM offers the advantage that the writing voltage and tip-to-substrate spacing can be controlled independently, whereas with STM the two parameters are integrally linked.
Compared with Scanning Electron Microscope, AFM provides extraordinary topographic contrast direct height measurements and unobscured views of surface features (no coating is necessary).
Compared with Transmission Electron Microscopes, three dimensional AFM images are obtained without expensive sample preparation and yield far more complete information than the two dimensional profiles available from cross-sectioned samples.
Compared with Optical Interferometric Microscope (optical profiles), the AFM provides unambiguous measurement of step heights, independent of reflectivity differences between materials.