This study generates novel manifold microchannel heat sink structures for high heat flux cooling, by applying topology optimisation within a multi-objective 3D conjugate heat transfer model. Compared to rectangular manifold microchannels, the proposed structures reduce pressure drop by 17 % (7.2 kPa - 6.0 kPa) by suppressing stagnation regions, and a more substantial 79.2 % (5.8 kPa - 1.2 kPa) by also limiting nozzle constrictions. This structure simultaneously reduces thermal resistance by 22.4 % (0.148 W/cm²K – 0.115 W/cm²K) by introducing intricate pins and constrictions, which augment jet impingement and counteract streamwise heating of the fluid. This study reveals some topology optimisation deficiencies: manual tuning of conditions, penetration of fluid to solid, and discrete geometry extraction. However, the resulting structures demonstrate how the topology optimisation process may leverage advances in additive manufacturing to extend the capabilities of high heat flux coolers.