A controller for an electro-mechanical actuation system (e.g., missile fin actuator) includes a Kalman estimator circuit generating an estimate of operating state including position and velocity of motor, position and velocity of a position-controlled element (PCE), and motor current. The estimate is generated based on a dynamic model explicitly including the effect of structural stiffness and damping in the coupling between the motor and PCE, for example by treating it as a mechanical oscillator having spring and damping constants. The Kalman estimator operates on a motor drive control signal and a measured position signal which may be from a Hall sensor sensing motor position. A linear quadratic regulator circuit applies a state feedback gain matrix to a state vector to generate a control effort signal. The state feedback gain matrix minimizes a quadratic cost function representing variance of the control effort signal and/or the measured position signal.