A novel thermoplastic fusion bonding method using a pressure-assisted boiling point (PABP) control system was developed to apply precise temperatures and pressures during bonding. Hot embossed polymethyl methacrylate (PMMA) components containing microchannels were sealed using the PABP system. Very low aspect ratio structures (AR = 1/100, 10 μm in depth and 1000 μm in width) were successfully sealed without collapse or deformation. The integrity and strength of the bonds on the sealed PMMA devices were evaluated using leakage and rupture tests; no leaks were detected and failure during the rupture tests occurred at pressures greater than 496 kPa. The PABP system was used to seal 3D shaped flexible PMMA devices successfully.