The foundations of most large industrial machines are complicated in configuration and shape that result in difficulties of modal testing and finite element modeling. Pseudo Mode Shape Method (PMSM) needs only the measurements of frequency response functions at the joint interfaces of the substructure and the mother structure to develop the equivalent dynamic matrices (called the pseudo matrices) of mass, damping, and stiffness of the substructure, which greatly simplifies the modeling procedure of the complicated substructure. Experimental validation of PMSM was conducted by modeling the foundation of a rotor-bearing-foundation system. The foundation is regarded as the substructure and modeled by PMSM. The rotor is the mother structure and modeled by finite element method using 3D Timoshenko beam elements. The effects of rigid body modes of PMSM in this experiment are also investigated.