With the increase in the chip packaging density the amount of heat generated from them has also increased considerably. Conventional cooling techniques are not well suited to solve the thermal problems that are arising as a result of this miniaturization of power microelectronic devices. We have developed a novel assembly of micro-pipe laden heat conducting substrate and thick film thermoelectric micro-cooler to deal with this issue. This paper presents the description of the novel micro-cooler fabrication technique and the results of the thermal analysis done on the micro-pipe laden substrate using the Pro/Mechanica thermal simulation package for varying performance factors.