The best way is to hold the layers apart at one end and pressure roll from the other. If the pieces are too rigid it will be more difficult. It is important to bring the pieces into conformal contact very slowly. If you bring them into contact too quickly, you will trap air in between. Essentially, once you get within a couple microns the pressure required to move the air from between the layers becomes very high, then when the outer edges touch, the air cannot escape and bubbles are formed.

If your layers are very flexible, you should be able to measure a thickness variation or some surface deformation that will indicate the location of the bubbles (assuming that the layers are very flat).

Could you provide more information about the material and it's thickness and flexibility?

Vacuum.

You may apply the principle "air against air" , namely, the soft loading of your layers using elastic spherical shell under increasing internal presure (pneumatic loding) .  Then the bubbles will move apart from the centre of initial contact to edge of contact and remove out.

Serge

http://www.smooth-on.com/faq_display.php?faq_id=3

http://www.instructables.com/id/Make-a-good,-cheap,-upgradeable-sheet-plastic-vacu/

Dear All, 

Thank you so much for your quick and thorough responses. I have figured out the problem which was due to the incorrect process which I was using to load the layer, as Dr. Serge and Dr. Al-Mosawi indicated.   Dr. Reiserer was also very helpful in recommending to measure thickness variation to identify the location of the bubbles.  Again, I appreciate all your comments and suggestions.  

Best regards, 

Antonio Tito