Some robots are designed to be lightweight and flexible, enabling them to access small and challenging paths in various applications. These features enable robots to collaborate with humans in performing specific production tasks. However,the movement of the flexible manipulator can become self-excited when handling a cutting tool on a workpiece, which can lead to a control problem. This article presents a control solution for lightweight robotic manipulators with rotating tools, such as polishing and milling, using smart actuators. The control discretization method is also introduced to facilitate integration into digital controllers. The paper starts by describing the governing equations of the non-ideal flexible manipulator for polishing and milling and analysing its dynamic behavior. Subsequently, models for the controllers of the DC motor-only actuators and the hybrid (shape memory alloy and DC motors) actuators were formulated using shape memory alloy and a suboptimal control scheme known as the discrete state-dependent Riccati equation. The coupled system was analysed dynamically, and it was observed that it exhibits chaotic behavior. The results suggest that incorporating smart actuators into the motor group of the system could decrease the positioning error of the manipulator and significantly reduce the oscillation of the robot’s end-effector.