A microcapillary pumped loop (MCPL) utilizing a two-phase heat transport has been investigated extensively because of its high heat transmission ability. Although the MCPL has been started up successfully, the initial amount of working liquid required to fill the system is so hard to control that the repeat operation of MCPL is not easy to initiate. In addition, the issue of Newton ring often occurs in the thermal bonding process of the chip and even causes the device to crack. An innovative method of micromatrix posts is proposed and confirmed by experiment for eliminating the initial filling and Newton’s ring effectively. This proposed method will be useful in the operation of MCPL and all thermal bonding of microchips.