Single micro pin-fin configurations having the same chord thickness/diameter but different shapes are numerically modeled to assess their heat transfer and hydraulic performances for Reynolds number values changing between 20 and 120. The configurations are three-dimensionally modeled based, and their heat transfer performances are evaluated using commercially available software COMSOL Multiphysics 3.5a. Navier-Stokes equations and continuity and energy equations are solved under steady-state conditions for single-phase water flows. To increase the computational efficiency, half of the domain consisting of a micro pin-fin located inside a microchannel is modeled using a symmetry plane. To validate the model, experimental data available in the literature are compared to simulation results obtained from the model of the same geometrical configuration as the experimental one. Accordingly, the numerical and experimental results show good agreement. Furthermore, performance evaluation study is performed using three-dimensional (3D) numerical models in the light of flow morphologies around micro pin-fins of various shapes. According to the results obtained from this study, the rectangular-shaped micro pin-fin configuration has the highest Nusselt number and friction factor over the whole Reynolds number range. However, the cone-shaped micro pin-fin configuration has the best thermal performance index, indicating that it could be more preferable to use micro pin-fins of unconventional shapes in micro pin-fin heat sinks.