The atomic force microscope (AFM) is developing into a very general tool for exploring biological surfaces. At present there are four broad areas of applications for the AFM: imaging surfaces, manipulating surfaces, measuring intermolecular forces and determining micromechanical properties. Because the dimensions of the apex of the tip used are typically on the order of 10's of nanometers, local measurements of properties are possible on a much smaller length scale than previously. Several reviews that provide further details on AFM instrumentation and biological applications have been published. These reviews also provide specific references for the range of applications that will be reviewed in this tutorial.AFM imaging modes can be divided into two groups based on the detection method, the DC method detects the absolute deflections of a cantilever while the AC method detects the RMS amplitude of an oscillating cantilever. Conventional contact AFM, sometimes called repulsive mode, is based on DC detection of the cantilever movement as the tip moves across a surface, usually in direct contact with the surface. The deflection of the cantilever is used to control the height of the sample, and the force applied to the sample, through a feedback loop.