Polymers have the obvious advantages of flexibility in design and cost effectiveness to fabricate a lab-on-a-chip (LOC) device. Polyether ether ketone (PEEK) in particular is very attractive choice as it adds biocompatibility in addition to the possibility of hematic sealing in a 3D design. Hereby, we extend our previous successful technology of autohesive hermetic bonding of medical implants into lab-on-a-chip devices. We explore a conceptual 3D micro channels design with hermetic potential using PEEK and PS sheets. A hermetic and mechanically strong (through tensile test) 3D multilayer device was obtained using plasma treatment with oxygen and methane as precursors followed by pressing at temperature near of Tg + 20 of the polymer with the lowest Tg (PS). This nanotexturing technique is also used to facilitate thermal and mechanical stability of the microchannels for microfluidic applications. X-ray tomography measurements showed that 3D polymer made chips, at certain plasma and press bonding conditions, have structural integrity and no deformation were detected in channels shape post thermal pressing process. The dimension stability of channels and reservoirs and the rigid interfacial region at PEEK-PS make this chip design attractive and feasible for advanced lab-on-a-chip applications.