There is currently a large effort underway to understand the physics of avian-based flapping wing vehicles, known as ornithopters. There is a need for small aerial robots to conduct a variety of civilian and military missions. Efforts to model the flight physics of these vehicles have been complicated by a number of factors, including nonlinear elastic effects, multi-body characteristics, unsteady aerodynamics, and the strong coupling between fluid and structural dynamics. Experimental verification is crucial in order to achieve accurate simulation capabilities. A multi-disciplinary approach to modeling requires the use of tools representing individual disciplines, which must be combined to form a comprehensive model. In the framework of this research a five body flexible vehicle dynamics model and a novel experimental verification methodology is presented. For the model development and verification of the modeling assumptions, a data set providing refined wing kinematics of a test ornithopter research platform in free flight was used. Wing kinematics for the verification was obtained using a Vicon motion capture system. Lagrange equations of motion in terms of a generalized coordinate vector of the rigid and flexible bodies are formulated in order to model the flexible multi-body system. Model development and verification results are presented. The `luff region" and "thrust flap region" of the wing are modeled as flexible bodies. A floating reference frame formulation is used for the ornithopter. Flexible body constraints and modes are implemented using the Craig-Bampton method, which incorporates a semi-physical subspace method. A quasi-steady aerodynamic model using Blade Element Theory was correlated and verified for the problem using the experimental wing kinematics. The aerodynamic model was then formulated in terms of generalized coordinates of the five-body flexible multi-body system and is used in the resulting model in order to account for aero-elasticity. Modeling assumptions were verified and simulation results were compared with experimental free flight test data.