The origin of contrast in atomic force microscopy (AFM) lies in the probe's response to forces between itself and the sample. These forces most commonly result from changes in height as the tip is scanned over the surface, but can also originate in properties inherent in the sample. These have been exploited as further means of contrast and have spawned an array of similar imaging techniques, such as chemical force microscopy, magnetic force microscopy, and frictional force microscopy. All of these techniques use AFM as an extremely sensitive gauge to map forces at discrete sites on the surface. A natural extension of this approach is to map forces in an array, in order to create a force map. AFM can be used in aqueous or fluid environments, thus allowing the exploration of forces in biological systems under physiologically relevant conditions. By immobilizing one half of an interacting pair of proteins onto the tip and the other half onto the substrate, it is possible to investigate the electrostatic and hydrophobic interactions between them. We employed these techniques to examine the interaction between a pair of proteins of known affinity that are involved in exocytosis (NSF and alpha-SNAP) and separately to demonstrate how two-dimensional force mapping can be applied to the nuclear envelope to identify nuclear pore complexes.