Thanks, Everyone!
  A lot of people gave me bunches of useful suggestions on how to get rid
of the bubbles in the microfluidic devices.
  I will post the suggestions here as a summary.
  1. From Thilo Semperowitsch :
  you may try an additional plasma to get surfaces that are all
hydrophilic.
To a certain extent you can "refresh" plasma treated surfaces, that spent a
long time at ambient. Microwave plasma works very nicely even in small
cavities, as the radicals will cause the surface treatment and not an ion
bombardment.

Another way might be to fill your device under vacuum (make sure that the
liquid is properly degased as well!).
  2. From Anpan Han
  You might try to fill the device with ethanol first and change the
reservoir
with what ever buffer. Then use vacuum to remove the ethanol and drag the
buffer into your system. Ethanol have better wetting properties than water.

Hope this helps.
  3. From Manscher Martin
  Trapping bubbles, removing bubbles etc. in microfluidic devices is
almost a science in itself (with many articles, patents etc.). The
simplest way is de-gassing the liquid in advance, by pumping on it and
exposing it to ultrasound. If you can accept the presence of the
bubbles, having the liquid run around it, another primitive solution you
could try is that sketched in "A unique solution for preventing clogging
of flow channels by gas bubbles", Kohnle et al, IEEE?? 2002, p. 77

http://www.imtek.de/content/pdf/public/2002/solutionpreventingcloggingfl
owbubbles.pdf
  4. From Danny Klein:
  Another simple way to degas the fluid is to boil it in advance, pump out
the
gases, keep the liquid in a sealed vessel and cool it down before use.
This way the liquid will be degassed and remain that way, at least till you
have injected it to your micro-device.

  Thank all of you for the suggestions. Good night!

  Jason