The fabrication of polymer microchips allows inexpensive, durable, high-throughput and disposable devices to be made. Poly(methylmethacrylate) (PMMA) microchips have been fabricated by hot embossing microstructures into the substrate followed by bonding a cover plate. Different surface modifications have been examined to enhance substrate and cover plate adhesion, including: air plasma treatment, and both acid catalyzed hydrolysis and aminolysis of the acrylate to yield carboxyl and amine-terminated PMMA surfaces. Unmodified PMMA surfaces were also studied. The substrate and cover plate adhesion strengths were found to increase with the hydrophilicity of the PMMA surface and reached a peak at 600 kN m(-2) for plasma treated PMMA. A solvent assisted system has also been designed to soften less than 50 nm of the surface of PMMA during bonding, while still maintaining microchannel integrity. The extent to which both surface modifications and solvent treatment affected the adhesion of the substrate to the cover plate was examined using nanoindentation methods. The solvent bonding system greatly increased the adhesion strengths for both unmodified and modified PMMA, with a maximum adhesion force of 5500 kN m(-2) achieved for unmodified PMMA substrates. The bond strength decreased with increasing surface hydrophilicity after solvent bonding, a trend that was opposite to what was observed for non-solvent thermal bonding.