Let me explain,

Lets say I used Jed's Half-Life Model Viewer to decompile the default Garand model. If you look at all the .bmp files you will see the skin itself "unwrapped" so to speak. Anyway, one of those bmp files is where the rear site of the Garand is and the middle of it is blue in color, but supposed to the transparent. My question is, how do I get it to be transparent as a bmp file so it doesn't show up ingame with a blue dot?

Try this: http://collective.valve-erc.com/index.php?doc=1043360861-70912800 :)