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In this work, a design methodology which combines CFD with a mathematical optimisation algorithm (a leapfrog optimisation program and DYNAMIC-Q algorithm) is proposed. This automated process is applied to three design cases. In the first design case, the peak wall temperature of a microchannel embedded in a highly conductive solid is minimised. The second case involves the optimisation of a double row micropin-fin heat sink. In this case, the objective is to maximise the total rate of heat transfer with the effect of the thermal conductivity also being investigated. The third case extends the micropin-fin optimisation to a heat sink with three rows. In all three cases, fixed volume constraint and manufacturing restraints are enforced to ensure industrial applicability. Lastly, the trends of the three cases are compared. It is concluded that optimal design can be achieved with a combination of CFD and mathematical optimisation.