I used photoshop for most of the dds textures editing.
1. Open said files , preferably in BMP.
2. Select 'Magic Eraser' and click on the part you want to set transparent.
3. Save as *.dds
4. Import the *.dds into your map.
My projects : The Hammer of Dawn, Noir : Automata, Noir : Evolution, Noir : Ascension
Many awesome projects : Custom Campaign Initiative
Something for the community : A Small Letter of Thanks, SC2mapster Classic Skin - Alevice