In this paper the problem of 3D physiological motion compensation in beating heart surgery is resolved by an adaptive control architecture based on Model Reference Adaptive Control (MRAC). The proposed control architecture uses the measures of the contact efforts applied by the surgical tool on the heart to assure force feedback. No apriori information about motion characteristics is necessary. It includes a nonlinear feedback linearizing the robot dynamics and a velocity loop. Simulation results are presented to show the effectiveness of the proposed control architecture for 3D compensation of physiological motions in beating heart surgery. Furthermore, its robustness toward uncertainties on dynamic parameters and environment stiffness is shown.