Nanoindentation is a popular experimental technique for characterization of the mechanical properties of soft and biological materials. With its force resolution of tens of pico-Newtons, the atomic force microscope (AFM) is well-suited for performing indentation experiments on soft materials. However, nonlinear contact and adhesion complicate such experiments. This paper critically examines the application of the Johnson-Kendall-Roberts (JKR) adhesion model to nanoindentation data collected with an AFM. The use of a nonlinear least-square error-fitting algorithm to calculate reduced modulus from the nanoindentation data using the JKR model is discussed. It is found that the JKR model fits the data during loading but does not fit the data during unloading. A fracture stability analysis shows that the JKR model does not fit the data collected during unloading because of the increased stability provided by the AFM cantilever
