The present study uses a reduced domain model to evaluate the impact of varying micro-pin fin (MPF) shapes on the thermal and hydrodynamic performance of a silicon micro-gap embedded with MPFs. The MPFs of circular, ellipse and teardrop shapes with a constant height and diameter perpendicular to the flow direction are analyzed for a staggered arrangement with 24 and 126 MPFs in the hotspot and background zones, respectively. A fixed heat flux of 250 W/cm² is set at the background zone, while the hotspot heat flux is varied in the range of 250-750 W/cm². The thermo-hydraulic characterization is done by evaluating the pressure drop, temperature profile, velocity contour and streamlines for detecting the flow separation and wake region. The results show that the teardrop MPF has the highest pressure drop, which is the minimum for ellipse fins. Early flow separation with extended wake region is seen for teardrop MPF, resulting in higher pressure drop. The micro-pin fin heat transfer performance is controlled by the area of heat transfer and flow separation with the extent of the wake region. The circular MPF has the lowest heat transfer performance compared to other fins, as it has the smallest surface area for heat transfer. As the ellipse and teardrop fins have nearly equivalent surface areas, the trade-off results of controlling parameters dictate the heat transfer performance.