Trajectory tracking with flexible systems is extremely difficult. This difficulty is increased when there are unobservable modes. Optimal PID control can be used for standard trajectory tracking, whereas sliding mode control can be used in systems with parametric uncertainties. Command shaping has been proven to be beneficial in eliminating unwanted vibration. This paper shows that command generation can be utilized to eliminate unwanted vibration from a system with an unobservable mode. Both optimal PID and sliding mode control can be used in conjunction with command generation for enhanced system performance.