How do you add see-trough spots in textures?

To do this, yes you can just paint the spots out in an alpha channel, or you can just erase the parts from the main texture, and leave a transparent background.

[Blocked Image: http://i.imgur.com/mN6OVw4.png]

I'm assuming by "not working", the material just seems to be incorrectly / not displaying the transparency in game, if this is the case, you can follow this little guide.

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1) Export your texture as a .png (it doesn't have to be png, anything that supports transparency.)

2) Using VTFEdit, import the texture using these parameters:

[Blocked Image: http://i.imgur.com/bgSMXDk.png]

3) Once you have created the VTF and VMT through VTFEdit, add "translucent" 1 to the vmt

[Blocked Image: http://i.imgur.com/BGUgKJq.png]

$translucent can cause some issues, and if the material doesn't fade from solid, to partially transparent to transparent, you should use $alphatest instead. This works well where materials have clean cut holes into them, like the image you posted from nuke.

[Blocked Image: http://i.imgur.com/r2SbXLR.png]

And here is an image from VDC explaining the problems with translucent

[Blocked Image: https://developer.valvesoftware.com/w/images/3/3a/Translucent2p.png]

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Hope this helps!