Chain molecules consisting of -CH2- groups with slightly bulky end groups -CH3 are chemically simple objects, which have some attractive features for AFM studies. First of all, alkane layers on graphite can be used as standard and calibration samples for imaging in the sub-100 nm scale. In addition, these objects can be also considered as primitive heterogeneous system or primitive block copolymer in which -CH3 groups and -CH2- represent "blocks" dissimilar in their size, mobility and mechanical properties. This is a reason that these groups exhibit different contrast in he AFM images.

Other interesting feature is an alkane arrangement on different substrates, which is a result of competition between alkane molecules interaction with a substrate and their crystallization behavior. Therefore, alkane molecules either align parallel to the surface or they form crystals with chains oriented perpendicular to the substrate. AFM is one of few techniques than can be used for characterization of these objects and their various transformations. The alkanes and, especially, those with ultra long chains with number of carbon atoms over 100 are excellent models of polyethylene - one of mass-produced polymer. AFM studies of chain folding, crystallization and melting in ultra long alkanes offer unique information about similar processes in this and other polymers.

Use of most sharp probes is always preferable for high-resolution studies of alkane layers. Yet the sharp tips can be less subjective to damage when softer cantilevers are used. Therefore probes with sharp tip should have stiffness less than 5 N/m. Actually, because sharp tips experience less adhesive interactions therefore probes with such tips can have very soft cantilevers and still be applied for tapping measurements. See high resolution imaging for details.