Pneumatic vibration isolation tables are used in the field of semiconductor manufacturing and precision measurement. The flow disturbance to the isolation table causes the fluctuation of the table. In order to control the flow disturbance, multi-connection air regulators are often used. However, the multi-connection air regulators lead to a pressure loss of the compressed air. Previously, we used two feedforward control methods which utilized a pressure sensor to measure the supplied air pressure and provide feedforward controlled signals to the actuators. One method used an air spring and the other used a voice coil motor (VCM) as the actuators. The current study proposes flow meter instead of pressure sensor for the feedforward control of the flow disturbance. Until now, a flow meter has been used for monitoring the supplied air flow to the pneumatic isolation table. The objective of this study is to utilize a flow meter in practical control of the flow disturbance. In addition to the control of flow disturbance, the proposed method is also used to control the disturbances caused by the reduced supplied flow and air flow drops.