Someone asked me how to do this so I wrote this up and decided to post it here in case anyone else was interested.
When you open your model in Milkshape,
whatever groups you want to have transparent textures should be named
accordingly. *yourshipsname*_glass (I usually use my ships name, or an abbreviation
of it, but it doesn't matter as long as it is unique and ends with _glass)
Now create a new material in the milkshape materials tab. Leave the color as it is,
but rename it *yourshipsname*_glass. Now assign this texture to any group you want
to be a transparent window.
Once you are finished assigning all your textures, (The rest should be like normal)
you can export your mat file. When you go to export it, it should not be able to find a
file linked to your blank material. So it will ask you to direct it to one, just hit
cancel on this window we do not need a file there.
Once the export is complete open your mat in the UTF editor.
Look under the material library for your glass material, mine looked like cvds_glass
Click on the plus sign to expand your glass texture, and it should present you
with three more options. DC, OC, and Type
Material Library:
cvds_glass
Click on Dc
Edit Float array
You should see four sets of numbers.
One zero with seven zeros behind the decimal point.
These each represent a color. 0.999999 in the second line will
produce a really strong green color, 0.111111 a really weak
green color.
You can change these values as you see fit to blend different colors.
For instance, this will give you the orange, brown color used on most civilian
ships.
0.654902
0.529412
0.317647
0.000000
Next click on Oc
Edit Float Array
You should see two sets of numbers
0.000000
0.000000
You only need to worry about the first set, leave the second one set to all zeros.
The first set will be the opacity of the texture. This is how transparent it
will be. 0.999999 will be very solid, you won't be able to tell if is transparent
for the most part. 0.111111 will almost look like the window doesn't exist at all.
I like to use somewhere between 6-8. Mine looked something like this,
0.800000
0.000000
Type
Last but not least is type, for the most part you shouldn't have to worry about
this if you imported it the way I mentioned above. This can cause you a lot of
headaches. So I would suggest not editing it at all.
When you are finished hit save and if done correctly you should have a new transparent window on your ship in game.