The Floating Frame of Reference (FFR) formulation is a well-established and reliable method for modeling flexible multi-body systems. The FFR formulation has been adopted for dynamic systems that are characterized by large rotations with relatively small deformations. Many scientific papers have pointed out these characteristics with the scrutiny of the simulation results and comparisons with other modeling techniques. However, the FFR is still enclosed in the theoretical aspects and simulation work and faces difficulties when being applied to practical systems. The crucial point in these difficulties centers on coordinate reduction and the associated mapping between nodal and modal coordinates. The process of selecting the necessary modes may be theoretically simple, but the situation is different when applied in a real operational environment. The strategy developed in this work combines the Operational Modal Analysis, specifically the Frequency Domain Decomposition (FDD) approach, and the FFR formulation to build a suitable model of practical multi-body systems. The output model has been validated experimentally. The results show that the proposed FFR-FDD method can be efficiently used to construct multi-body models for those systems that work in premise operational conditions.