Surface irregularities are often seen when using the scanning electron microscope, but these are absent using the AFM. One such analysis is described below: Occasionally, the cartilage surface exhibits local discontinuities where an underlying fibrous network is distinguishable. Digestion of the cartilage surface with chondroitinase AC exposes this fibrous network more systematically so that the individual fibers are visualized with great clarity by AFM. When imaged at higher magnification, these distinct fibers exhibit a 60nm repeat, indicating that they are assembled from collagen fibrils. (Miller, Aebi, and Engel para. 4)

The AFM has been shown to be valuable in similar analyses of biological materials and processes. While AFM images also offer a view of the atomic detail of solids, the process is not useful for analyzing biomolecules such as proteins because they are designed to undergo conformational changes and form flexible supermolecular assemblies, meaning they are mechanically "soft" so that the surface cannot be probed for atomic detail. However, as Miller, Aebi, and Engel note, "state-of-the-art specimen preparation and instrumentation now allow the surface topography of native proteins to be imaged at subnanometer resolution" (para. 5).

A recent example of biological research using the AFM comes from Santa Barbara, California, where researchers used the AFM to discern unique properties of bone:

Collagen, the most abundant protein in the human body -- serving as a structural component of a variety of tissues including bone, tendon and skin -- reveals special properties which allow it to "bounce back" when pulled or stressed in laboratory experiments. The AFM operates by tapping and pulling with a tiny needle. ("Bone Strength Probed by Scientists" para. 1)

This research shows that the collagen in bone contains sacrificial bonds that rupture as the collagen is stretched, and these ruptures then heal. The purpose of these bonds is to provide a means for dissipating mechanical energy in collagen molecules (("Bone Strength Probed by Scientists" para. 2).

AFMs constitute a subset within the larger group known as scanning-probe microscopes, which can utilize many different types of tips to measure electrical, mechanical, or magnetic properties. Tips exist that can perform simultaneous dimensional and electrical measurements. It is when a scanning-probe microscope uses a tip that can discern properties at the atomic level that the instrument becomes an atomic-force microscope. Such devices can measure features within a few Angstroms and do so without harming the sample. As on scientist notes, "Manufacturers need to perform nondestructive measurements in all three dimensions to ensure their device geometries fall within ever-smaller tolerances" (Titus para. 4). Another company uses AFM to detect flaws in surface-acoustic-wave devices, defects that cannot be seen with an optical microscope. The same company uses AFM to check the results of steps in photolithograpy (Titus paras 5-6).

Kevin Kjoller considers how to measure the true resolving power of an atomic force microscope, noting first that resolution means the same as it does for an optical microscope, meaning the minimum distance between two adjacent objects that a microscope can identify as separate. Kjoller complains that most manufacturers substitute some meaningless term for resolution and ignore the reality. Several issues need to be considered, such as the size of the probe and three types of limiting noise, electical, mechanical, and acoustic. Kjoller defines electtical noise as "the sum of the thermal and operating noise from all components inside the AFM electronics, including any noise due to cross-talk and less-than-optimal grouping" (Kjoller para. 7). Mechanical noise can be particularly harmful and may derive from the mechanical path length between...

Acoustic noise means that the system generates noise, and this can be eliminated with a well-designed and well-implemented acoustic isolation environment" (Kjoller paras. 8-9).
The accuracy of the AFM depends on the state of the tip, and a worn tip can produce blurred images ("V-shaped Tips Blur Microscopy" paras. 1-7). Efforts to control for this include the recent development of an automatic tip evaluation system showing when the tip needs to be replaced ("Automatic Tip Evaluation Broadens AFM Applications" para. 1).

More and more applications for the AFM are developed all the time. Scientists have found many ways to make use of the unique capabilities of this system to analyze different substances down to the atomic level.