Atomic force microscopy (AFM) was developed in 1986. It is an important and versatile surface technique, and is used in many research fields. In this review, we have summarized the methods and applications of AFM, with emphasis on nanofabrication. AFM is capable of visualizing surface properties at high spatial resolution and determining biomolecular interaction as well as fabricating nanostructures. Recently, AFM-based nanotechnologies such as nanomanipulation, force lithography, nanografting, nanooxidation and dip-pen nanolithography were developed rapidly. AFM tip (typical radius ranged from several nanometers to tens of nanometers) is used to modify the sample surface, either physically or chemically, at nanometer scale. Nanopatterns composed of semiconductors, metal, biomolecules, polymers, etc., were constructed with various AFM-based nanotechnologies, thus making AFM a promising technique for nanofabrication. AFM-based nanotechnologies have potential applications in nanoelectronics, bioanalysis, biosensors, actuators and high-density data storage devices.