In the present work, micro-protruded patterns on flush mounted heat sinks for convective heat transfer enhancement are investigated and a novel methodology for thermal optimization is proposed. Patterned heat sinks are experimentally characterized in fully turbulent regime, and the role played by geometrical parameters and fluid dynamic scales are discussed. A methodology specifically suited for micro-protruded patterns optimization is designed, leading to 73 % enhancement in thermal performance respect to commercially available heat sinks, at fixed costs. This work is expected to introduce a new methodological approach for a more systematic and efficient development of solutions for electronics cooling.