Drag reduction by means of flow control is investigated for supersonic base flows at Mach number M = 2.46 using Direct Numerical Simulations (DNS) and the Flow Simulation Methodology (FSM). The objective of the present work is to understand the evolution of coherent structures in the flow and how flow control techniques modify these structures. For such investigations, simulation methods that capture the dynamics of the large turbulent structures are required. For transitional base flows at ReD = 30,000 DNS are performed. Due to the drastically increased computational cost of DNS at higher Reynolds numbers, a hybrid RANS/LES method (FSM) is applied to simulate base flows with flow control at ReD = 100,000. Active and passive flow control techniques that alter the near-wake by introducing axisymmetric and longitudinal perturbations are investigated. A detailed analysis of the dynamics of the resulting turbulent (coherent) structures is presented.