Results of numerical simulation of flow field and heat transfer due to submerged multiple circular jets impinging on a target surface with protrusions, at orifice plate to target spacing smaller than twice the jet diameter, are presented. The spent fluid is either locally extracted using effusion holes or allowed to flow outwards through the side walls. The study establishes a methodology to systematically modify the impinging surface based on the local fluid-flow structures. The effect of protrusions on the flow field and heat transfer is studied for varying protrusion sizes and locations at Reynolds numbers in the range of 1,000 to 10,000. It was found that addition of protrusions improves the heat transfer characteristics of the system, lowering the average heater side-temperature as well as the energy required to pump the fluid per unit amount of heat removed.