This paper proposes a novel, fast, and automatic modeling method to build a virtual model with minimum degrees of freedom (DOFs) without the need for FE models or human judgment. The proposed program uses the iterative closest point (ICP) algorithm to analyze the mode shape vector of structural dynamic characteristics to define the position and DOFs of the joints between structural components. After the multi-body dynamics model was developed in software, it was converted into an SSM to connect the servo loop model. Then, the mechatronic integration analysis was performed to verify the dynamic characteristics of the tool center point (TCP) and the workbench in the experiment and simulation. The model created by the proposed identification process has a small DOF and can accurately simulate the dynamic characteristics of a machine. This model can be used for dynamic testing and control strategy development in mechatronic integration.