The fourth industrial revolution led to advanced servo systems, enhancing productivity across industries. However, designing these systems remains challenging due to the performance-stability trade-off. This paper presents a model-based motion control of a linear motor motion stage in frequency domain. A user-code for the PowerPMAC commercial controller was developed to excite motion control system so that we could get a frequency response. The theoretical frequency response of the servo algorithm was compared with the experimental frequency response. Based on this, a tuning graphical user interface (GUI) was developed to predict performance when the servo loop gain is changed. Especially, to compensate for residual vibrations caused by high acceleration and deceleration and to improve tracking error, DOB (Disturbance Observer) and ILC (Iterative Learning Control) control techniques were applied in the frequency domain. Through the design of the frequency domain motion controller, the control performance of the linear motor motion stage could be predicted with over 96% accuracy, resulting in a 54.32% improvement in tracking error and a 93.56% improvement in settling time, 85.29% in RMS error.