In this paper, two method were proposed for MDOF and different configuration bilateral system. First is the basic control architecture for MDOF systems. In this paper, the difference are clarified between conventional joint space based bilateral control and operational space control based on DTOB. In addition, the control architecture based on DFOB is proposed to improve the transparency of the system. As the second proposal, the scaling matrix design is also described for the master-slave system with different structure. The scaling for force and position information is designed based on the dynamic and kinematic model. Proposed scaling can match the scale in master-slave system, and it improves the operability of human operator. In addition, the advantage of the proposed DFOB based bilateral control architecture is also described. The validity of these two proposed methods are supported by several experiment results.