Drag reduction by means of flow control is investigated for supersonic base flows at M = 2.46 using direct numerical simulations and the flow simulation methodology. The objective of the present work is to understand the evolution of coherent structures in the flow and how flow control techniques can modify these structures. For such investigations, simulation methods that capture the dynamics of the large turbulent structures are required. Direct numerical simulations are performed for transitional base flows at ReD = 30,000. Because of the drastically increased computational cost of direct numerical simulations at higher Reynolds numbers, a hybrid methodology (flow simulation methodology) 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 structures is presented.