Force spectroscopy is a method to measure forces between the tip and the sample. In this method the topographic feedback loop is disabled, and the tip is ramped towards the surface, then back. During the ramp the amplitude or frequency shift (depending on the mode of operation) is recorded to show the strength of the interaction at different distances. Force spectroscopy was originally performed in amplitude modulation mode, but is now more commonly performed in frequency modulation. The force is not directly measured during the spectroscopy measurement, instead the frequency shift is measured which must then be converted into a force. The frequency shift can be calculated, by:
where  is the tips oscillation from its equilibrium position,  and  are the sensors stiffness and resonant frequency, and  is the amplitude of oscillation. The angle brackets represent an average of one oscillation cycle. However, turning a measures frequency shift into a force, which is necessary during a real experiment, is much more complicated. Two methods are commonly used for this conversion, the Sader-Jarvis method and the Giessibl matrix method.
For measurements of chemical forces the effect of the long range van der Waals forces must be subtracted from the frequency shift data. Originally this was done by fitting a power law to the long range tail of the spectrum (when the tip is far from the surface) and extrapolating this over the short range interaction (tip close to the surface). This fitting, however, is very sensitive to where the cut-off between long and short range forces is chosen, causing results of questionable accuracy. Usually the most appropriate method is to perform two spectroscopy measurements, one over any molecule under study, and a second above a lower section of the clean surface, then to directly subtract the second from the first. This method is not applicable to features under study on a flat surface as no lower section may exist.