If you have access to the alpha layer, then you can modify it's transparency.
This can only work on 2d images. Attempting to make a 3d texture transparent will only make it white.
Here is the shade bar for transparency.
Opaque ----- Translucent ----- Transparent
If the part of the alpha layer is pure black, it's completely transparent, and white making it completely visible.
Allm does not really take advantage of this, and Translucent windows have been rather unique in my experience.
Using the Shade bar, I put my windows alpha layer in LuniaImageSet1.dds in this shade.
My end result was this-
This works on any 2d textures, skills, the doodads on the map, buttons, windows, icons.. you name it.