What you'll need:
Adobe Photoshop, or your choice of editor.
The files you want to change, for this I'll use the recently released
[Only registered and activated users can see links. Click Here To Register...] since it's readily extracted and has .PSD files to make it even easier!
Step 1. Open your desired file(s) in Photoshop
Step 2. Select "Rectangular Marquee Tool" and select the whole file.
Step 3. Edit > Copy Merged.
Step 4. Channels > Create New Channel
Step 5. Edit > Paste Special > Paste into place
Step 6. Disable the View of RGB, Red, Green & Blue layers and select your Alpha Layer.
It will look something like this:
This is how it will look regularly if you open up a Targa file from in-game.
Alpha Layers work with White, Grey & Black only and this is how we set the transparency and it works like this:
Black (000000) = 100% Transparent
Grey = 1-99% Transparent
White (ffffff) = 0% Transparent
Depending on how transparent you want it you'll have to decide by using a grey color and using the Paint Bucket with 255 Tolerance. You'll want to keep the background Black otherwise it will show in-game as a white, this is why we keep the Pasted Layer selected like and only fill this with white/grey.
As I said, you just need to watch a few videos on YouTube to understand, it's very simple.