It depends on what graphics program you're using. In Gimp it's very easy*: use the eraser on the lowest layer to create transparent areas. Save as dds, setting compression to DXT5. Gimp require a dds plugin, which you can find on google.
U've to create an alpha channel in the canals option, which white color means what you see and black what u don't see.
Create it in the canals of the file, creating a new layer, it will name "alpha" for default, create ur color zones and then, save it as dx5 .dds.
Then u can use it importing on BTB or 3dsimed.... any u're using.
There's a nice tutorial on using alpha channels in Gimp on YouTube. I got used too much to Photoshop, then Gimp seemed to me little strange
Unfortunately my PS doesn't see dds plugin, but I use DDS Converter 2, which reads psd files with transparency. Strange, but when I add alpha channel to psd file, that Converter doesn't work to cooperate. I found a way for half-transparent images then - save them as .tga with alpha and DDS Converter is happy