This study presents an approach based on the floating frame of reference method to model complex three-dimensional bodies in a multibody system. Unlike most of the formulations based on the floating frame of reference method, which assume small or moderate deformations, the present formulation allows large elastic deformations within each frame by using the co-rotational form of the updated Lagrangian description of motion. The implicit integration scheme is based on the Generalized-alpha method, and kinematic joints are invoked in the formulation through the coordinate partitioning method. The resulting numerical scheme permits the usage of relatively large time steps even though the flexible bodies may experience large elastic deformations. A triangular element, based on the first order shear deformable theory, has been developed specifically for folded plate and shell structures. The plate element does not suffer from either shear or aspect-ratio locking under transverse and membrane bending, respectively. A stiffened plate element has been developed that combines a shear deformable plate with a Timoshenko beam. A solid element, that utilized the isoparametric formulation along with incompatible modes, and one-dimensional elements are also included in the element library. The tools developed in the present work are then utilized for detailed rotorcraft applications. As opposed to the conventional approach of using beam elements to represent the rotor blade, the current approach focuses on detailed modeling of the blade using plate and solid elements. A quasi-steady model based on lifting line theory is utilized to compute the aerodynamic loads on the rotor blade in order to demonstrate the capabilities of the proposed tool to model rotorcraft aeroelasticity.