actually you need something more sophisticated like gimp photoshop or paintshop pro for this.
I use photoshop and in photoshop you should select all the parts that you want to be transparent and then go to channels and add a new channel (alpha) then while you still in the new channel use a white brush to pain all over the picture (the selection only limits the color to the parts you want).
after that activate all of the channels and save it as TGA (make sure that in save options alpha channel is selected). voila the transparent HUD is ready.
if you don't understand these instructions search for tutorials on making alpha channels.
Pyramid entertainment - Play the game