The focus of this paper is topology optimization of fluid flow systems, particularly 2D laminar flows, widely found in microfluidic devices. The flow equations are solved numerically using a pseudo–spectral scheme and accurate derivatives are directly derived to facilitate gradient–based optimization. The proposed tool is utilized to enhance the performance of micro heat exchangers, in terms of minimizing the total pressure drop required to be supplied by micro pumps. It is well known that the geometry and arrangement of pinned fins play a pivotal role in total pressure drop of the system. Hence, in this work we aim to find the optimum topologies for various test cases by minimization of drag force on pined fins with a constraint on volume.