A fabrication and adhesion method for a polyaryl-ether-ketone (PAEK) device, such as a microfluidic device (400), is disclosed. At least one glassy uncrystallized PAEK substrate (250) is heated up to near or above the glass transition temperature to allow the substrate (250) to crystallize from the glass state, while embossing the substrate (250) with patterns (325). Bonding the PAEK substrate (250) to another substrate (255) is accomplished using a solvent-resistant adhesive (270), such as a polyimide-based adhesive, in combination with an adhesion enhancement treatment. In certain embodiments, the adhesion enhancement treatment is a plasma treatment or a chemical sulfonation treatment.