In this paper, a matrix perturbation technique is developed for flexible bodies (substructures) that undergo large reference translational and rotational displacements. Although the governing dynamic equations of motion of such systems are highly nonlinear because of the large angular rotations and the resulting nonlinear inertia coupling between the reference motion and the elastic deformation, a generalized linear eigenvalue problem that defines the deformation mode shapes of the body with respect to the selected body reference is identified. This eigenvalue problem is solved only once and the variations in the body stiffness and inertia properties due to a change in selected design parameters are evaluated by using perturbation analysis techniques. The main advantage of using the proposed technique is to avoid a new finite element discretization when some design parameters are changed. This, in turn, substantially reduces the computational time, especially when large scale flexible bodies with complex geometry are considered. A numerical example is presented in order to demonstrate the use of the perturbation techniques developed in this paper in the design of flexible multibody systems.