This paper concerns a SCARA robot with the flexible forearm linked to the rigid upper arm. The equations of motion are derived by the Lagrangian mechanics. For controller design, the perturbation approach is taken to separate the original equations of motion into linear equations describing small perturbed motions and nonlinear equations describing purely rigid motion of the robot. To effect the desired payload motion, open loop control inputs are determined based on the inverse dynamics of the latter. In order to reduce the positional error during maneuver, an active vibration suppression is done. To this end, a feedback control is designed for robustness against disturbance on the basis of the linear equations and the LQR theory modified to have a prescribed degree of stability. The proposed control scheme shows satisfactory performances in experiments as well as in numerical simulations.