This study presents the effects of adding an array of protrusions in a microchannel for heat transfer enhancement. The presence of mini-channels increases the overall heat transfer area and boosts the mixing development near the solid-fluid interaction; therefore, it can remove more heat than conventional mini-channels without protuberances. A numerical study proved that protuberances in a mini-channel increase the heat transfer performance by disturbing the relative fluid motion near the solid wall. The numerical simulation was performed with three different protuberances arrays: aligned, staggered, and angular. Each array consists of a thin flat plate with a hemispherical shape; the working fluid and the solid materials were water and copper. The study also includes the effect of different Reynolds numbers: 1,000, 1,500, and 2,000. Three heat inputs were applied in the numerical simulation; these were 1W, 3W, and 5W. The study was compared with a simple microchannel with non-protuberances to analyze the microchannel performance regarding heat removal and pressure drop. For heat transfer performance, the best array was the staggering array with a maximum heat removal increase of 5.26 percent. In terms of pressure drop performance, the best array was the aligned array, with a maximum increase of 34.73 percent.