The design, integration and certification of a store configuration to an aircraft/pylon involve extensive and expensive wind tunnel and flight testing with the objective of determining the operational and deployment envelopes for safe separation. Computational trajectory prediction techniques have been shown to have the potential not only to reduce the number of flight/wind tunnel tests but also to design an intelligent test matrix. In this paper, a commercial CFD tool, CFD-FASTRAN was used to predict the separation trajectories of two configurations of external stores. Coupled 6-DOF/CFD simulations using automated chimera-overset grid based methodologies were employed. The first configuration, a generic wing-pylon-store is compared with wind tunnel experiments at M=0.95. This demonstrated and validated CFD-FASTRAN’s compressible flow solver and 6-DOF motion models for store separation problems. The second case investigated the separation characteristics of a finned ADE store at M=0.5 and 0.95. The store trajectories and surface pressure distributions were computed and studied. The effect of the pylon diminishes as the store moves away and the dominant effect on the store is predominantly due to the surface pressure distribution from the oncoming flow on the store (sidewash).