In this paper, a model reference adaptive control for the atomic force microscope (AFM) of tapping mode is investigated. The dynamics between the AFM system and al sample is mathematically modeled as a second order spring-mass-damper system with oscillatory inputs. The attractive and repulsive forces between the tip of the AFM system and the sample are derived using the Lennard-Jones potential energy. By non-dimensionalizing the displacement of the tip and the input frequency, the chaotic behavior near a resonance frequency is better depicted through the non-dimensionalized equations. Four nonlinear analysis techniques, a phase portrait, sensitive dependence on initial conditions, a power spectral density function, and a Pomcare map are investigated. Because the equations of motion derived in this paper involve unknown parameter values such as the damping effect of the air and the interaction constants between materials, the standard model reference adaptive control is adopted. Two control objectives, the prevention of chaos and the tracking of reference signal, are pursued. Simulation results are included.