This article proposes a controller optimization for given disturbances, i.e., fluttering NRRO, RRO, sensor noise, and torque disturbance. This run-out oriented controller design is based on a response surface method and provides an optimal controller that minimizes positioning error due to the disturbances. The proposed method is not only for controller tuning but also gives us a cue to seek a direction about which disturbance we should prioritize to be reduced from a viewpoint of system integration.