In a previous work, magneto-rheological (MR) dampers were originally designed and implemented for reducing the vertical low-frequency vibration occurring in precise semi-conductor manufacturing equipment. To reduce the vibrations, an isolator levitated the manufacturing machine from the floor using pneumatic pressure which cut off the external vibration, while the MR damper was used to decrease the transient response of the isolator. However, it has been found that the MR damper also provides a damping effect on the lateral vibration induced by the high-speed plane motions. Therefore, in this work both vertical and lateral vibrations are controlled using the yield and shear stresses of the lateral directions generated from the MR fluids by applying a magnetic field. After deriving a vibration control model, an overall control logic is formulated considering both vertical and lateral vibrations. In this control strategy, a feedback loop associated with the laser sensor is used for vertical vibration control, while a feed-forward loop with the motion information is used for lateral vibration control. The experimental results show that the proposed concept is highly effective for lateral vibration control using the damping effect on multiple directions.