This paper describes a robust control scheme for high-speed and long stroke scanning motion of high precision linear motor system consisting of linear motor, air bearing guide and position measurement system using heterodyne interferometer. Nowadays, semiconductor process and inspection of wafer or LCD need high speed and long travel length for their high throughput and extremely small velocity fluctuations or tracking errors. In order to satisfy these conditions, linear motors actuating whole system must have enough thrust force. It is known that a linear motor with multi-segment magnet array(MSMA) makes larger thrust force than that with conventional magnet array. To gain larger thrust force with MSMA, Moon C1 Lee et al. performed the optimal design of MSMA linear motor. As a result of that, they improve the thrust force by 10%, but force ripple, which deteriorates the tracking performances and makes periodic position errors, becomes larger. So, force ripple must be compensated. To maximize the tracking performance of MSMA linear motor system, we propose the control scheme which is composed of a robust control method, TDC and a feedforward control method, ZPETC for accurate tracking a given trajectory and an adaptive ripple compensation algorithm(ARR) for estimating and compensating force ripple. The adaptive ripple compensation is continuously refined on the basis of tracking error. Using Lyapunov's Direct method, we prove the convergence and the stability of the proposed control scheme. Computer simulations and real-time experiment results verify the effectiveness of the proposed control scheme for high-speed, long stroke and high precision scanning motion and show that the proposed control scheme can achieve a superior tracking performance in comparison to conventional TDC control.