At present study, conjugate heat transfer effects of a free-ended micropillar within a channel was investigated numerically. There is a gap between pillar tip and upper channel wall while the pillar is attached to the end wall at the other side. Two design configurations were considered based on the heater location. In one design, the bottom channel wall where the pillar is attached is the heated surface while in the other design, the heater is located on the opposite wall of a pillar with tip gap. Also, a full height pillar attached to the ends walls from both sides is modeled as a baseline for comparison. In all designs, the heater was deposited onto a Pyrex substrate. Different tip gaps were investigated and results show that introducing free-ended pillar change the heat flux distribution over the heater. Average Nusselt number over the heated surface show a minimal decrease in both designs compared to the full pillar. Nusselt number in the wake region downstream the pillar significantly increases when the heater is located at the opposite side of the tip gap.