In high-precision positioning systems such as scanning machines, the feedback controller tuning needs a lot of time and skills. In particular, a feedback controller tuning with six-degree-of-freedoms (x,y,θz,z,θx,θy) is difficult because of the numbers of controller parameters in each axis. The feedback controllers designed as single-input single-output controllers in each axis may not achieve sufficient performance in multi-input multi-output systems, and stability may not be satisfied because of a coupling problem between each axis. The repetitive disturbance makes the performance worse in a constant velocity scanning motion, and they are conventionally rejected by a peak filter in other applications of high-precision systems such as a hard disk drive. In this paper, we propose a tuning method of a peak filter to suppress a repetitive disturbance which satisfies robust stability conditions for six-degree-of-freedom systems by using convex optimization. The effectiveness of the proposed method is verified by the error in the constant velocity scanning motion.