The precise control of spacecraft with flexible appendages is extremely difficult. The complexity of this task is magnified many times when several flexible spacecraft must be controlled precisely and collaboratively, as in formation flying. Formation flying requires a group of spacecraft to fly in a desired trajectory while maintaining both relative positions and velocities with respect to each other. This work enhances two current state-of-the-art formation flying algorithms, specifically leader-follower and virtual-structure architectures. First, a flexible satellite model is integrated into each of these architectures. Second, input shaping is used to generate the satellites desired trajectories, thereby enhancing the performance of the system. This dissertation addresses key issues regarding the application of command generation techniques to flexible satellites controlled with formation flying control architectures. The temporal tracking and the trajectory tracking of each architecture are examined as well as the vibration characteristics of the formation satellites. Design procedures for applying trajectory shaping for the leader-follower and virtual-structure architecture are developed. Experiments performed on a flexible satellite testbed verify key simulated results.