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The three dimensional circuit (3-D-IC) achieves high performance by stacking several layers of active electronic components vertically. Despite its impact on performance improvement, 3-D-IC also brings great challenges to chip thermal management due to its high heat density. Microchannel-based liquid cooling shows great potential in removing the high density heat inside 3-D circuits. The current microchannel heat sink designs spread the entire surface to be cooled with microchannels. This approach, though it provides sufficient cooling, consumes significant amount of extra cooling power. In this paper, we investigate the design of non-uniformly distributed microchannel cooling systems which provide sufficient cooling with less cooling power. The experiments show that, compared with the conventional design which spreads microchannels all over the chip, our non-uniform microchannel design achieves up to 80% cooling power savings.