I spent a long time trying to make .5mm holes through a .5mm pyrex wafer
as an access port for a fluidic device. At the end of the process we
found that  microabrasive powder blasting could be made to work. They
have a tool for this at the WTC which is dedicated for this purpose.
The advantage of this is that you can do patterns other than holes.

In my opinion this is a difficult process which is also very common in
micromachining and in need of a good textbook solution.

Here are some things I tried which did not work:

1. PECVD silicon etch mask for 49% HF. The PECVD silicon did not etch,
but it did flake off and contaminate the bath. Not fun to clean up.

2. Cr/Au etch mask for HF etch: same as above. Material flaked off.
Also, this material had lots of pin holes.

3. UV laser cutting. This was just slow. I don't remember the wattage or
the wavelength, but we didn't have success.

4. CO2 laser. This caused cracks in the wafer.

5. Drilling with a dremel and a diamond bit. This worked, but the
success rate was low, and we lost wafers in the process. At the end of
the drilling, the bit would break through the backside at times and
cause fractures in the glass.

6. Sand blasting with sand that was too large: this caused
micro-fractures in the glass.

I would recommend micro-abrasive powder blasting.

I believe that with the proper tooling diamond drilling can be made to
work. I would also like to hear about peoples experience with water-jet.

WTC recently got a new etch tool just for glass etching. My
understanding is that it will make verticle side walls at fine pitch,
but the masks only hold up for about 30um of etching. I have not worked
with this tool myself.

Thanks,
Rob MacDonald