F.e. in paint shop pro:
1. open image
2. with magic wand select those parts you want to have invisible
3. layers -> new mask layers -> show all
4. Fill this layer (selected areas) with black color
5. load/save mask -> save mask to alpha channel
6. go to mask menu (on the right) and delete this layer (black picture with white part inside)
7. answer NO for question about mask merged
8. save as .tga
end of story

Cheers