This paper presents a force model of the clean tube system, which was developed as a means of transferring air-floated wafers inside a closed tube filled with super clean air. The recovering force from the holes for floating wafers is modeled as a linear spring and thus the wafers motion is modeled as a mass-spring-damper system. The propelling forces are modeled as linear along with the wafer location. The paper also proposes a control method to emit and stop a wafer at the center of a control unit. It reveals the minimum value of the propelling force to leave from the control unit. In order to stop the wafer, it utilizes the exact time when the wafer arrives at the position to activate the propelling force. Experiments with the clean tube system built for the 12 inch wafer shows the validity of the proposed model and the algorithm.