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Metal-based microchannel heat exchangers (MHEs) are of current interest due to the combination of high heat transfer performance and improved mechanical integrity. Efficient methods for fabrication and assembly of functional metal-based MHEs are essential to ensure the economic viability of such devices. In this paper, the results on fabrication, assembly, and heat transfer testing of Cu- and Al-based MHE prototypes are reported. Efficient fabrication of Cu- and Al-based high-aspect-ratio microscale structures (HARMSs) has been achieved through molding replication using surface-engineered metallic mold inserts. Replicated metallic HARMSs were assembled through eutectic bonding to form entirely Cu- and Al-based MHE prototypes, on which heat transfer tests were conducted to determine the average rate of heat transfer from electrically heated Cu blocks placed outside the MHEs to water flowing within the molding replicated microchannel arrays. Experimentally observed heat transfer rates are higher as compared to those from previous studies on microchannel devices with similar geometries. The potential influence of microchannel surface profile on heat transfer rates is discussed. The present results illustrate the potential of metal-based MHEs in wide-ranging applications.