The clean tube system was developed as a means of transferring air-floated wafers inside a closed tube filled with super clean air. This paper presents a wafer position sensing method in the clean tube system, where the photo proximity sensors are used. The first presented method uses the two positions sensed lately in order to compute the wafer center position. The next method uses the latest sensed position and the next latest position compensated with the information of the wafer velocity. The third method uses the kalman filter, which enable us to use all the previous sensing information. The simulation results are compared to show results of the presented method. In addition, the paper presents a control method to stop the wafer at the center of the unit in the clean tube system. The experimental clean tube system worked successfully with the applying the both presented methods of sensing and control.