The drag associated with supersonic base flows is of critical importance for the design of aerodynamic bodies, such as missiles and projectiles. The base drag which accounts for a significant part of the total drag, that may be reduced by means of active and passive control of the near wake. There is evidence that large (turbulent) coherent structures evolve in these flows and strongly influence the mean flow. Therefore, in order to understand the dynamics of coherent structures in the wake and how flow control mechanisms modify these structures, numerical simulations were conducted. We performed Large-Eddy Simulations (LES) based on the Flow Simulation Methodology (FSM) for a Reynolds number of ReD = 100,000 and Mach number M = 2.46 using a high-order accurate research code, which was developed at the University of Arizona. Flow control mechanisms that alter the near wake by introducing axisymmetric and three-dimensional perturbations, thus emulating active and passive flow control were investigated. We also studied supersonic base flows at Reynolds number ReD = 3,300,000 and Mach number M = 2.46 using Detached-Eddy Simulations (DES). These investigations were performed using the commercial CFD-code Cobalt. In addition, for the same Reynolds number, we investigated Passive flow control using afterbody boat-tailing. Our results are compared to available experimental data.