Large Eddy Simulation (LES) with dynamic sub-grid scale eddy viscosity model has been applied to numerically investigate the evolution of complicated flow structures in supersonic base flow with mass bleed. Mean flow properties obtained from numerical simulations, such as axial velocity, pressure on the base surface, have been compared with the experimental measurements to show that LES is able to predict the mean flow properties with acceptable accuracy. The data obtained from LES has been further analyzed to understand the evolution of coherent structures in the flow field. Periodical shedding of vortical structures from the outer shear layer has been observed and it has also been found that this vortex shedding is associated with the flapping of the outer shear layer. The frequency of flapping of the outer shear layer has been found out and the phase-averaged streamlines have been analyzed to further study the evolution of vortical structures associated with this flapping. The phase-averaged streamline plots clearly elucidate the evolution of vortical structures along the outer shear layer. Further, the study of these structures is investigated by performing Proper Orthogonal Decomposition (POD) analysis of the data, obtained along the central plane in the wake region. The POD results also 2 seem to agree well with the observations made in the phase averaged streamline plots, as the concentrated energy and enstropy are observed in the outer shear layer with fewer POD modes.