This paper presents a geometric framework for analysis of dynamics of flapping wing micro aerial vehicles (FWMAV) which achieve locomotion in the special Euclidean group SE(3) using internal shape changes. We review the special structure of the configuration manifold of such systems. This work addresses to extend the work in geometric locomotion to the aerial locomotion problem. Furthermore, there seems to be limited work in modelling of flapping wing bodies in a geometric framework. We derive the dynamic model of the FWMAV using Lagrangian reduction theory defined on symmetry groups. The reduction is achieved by applying Hamilton's variation principle on a reduced Lagrangian. The resultant dynamics is governed by the Euler-Poincare and Euler-Lagrange equations.