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You can use it with any application (any .exe or .bat file like it says). What is it exactly that you need to use it for (i.e. what problems are you having with RC that you need to use 3D Analyze)?
I don't know if you have the BoPC version, but the BoPC one does not need the Disk, as only the Launcher runs a Disk Check, and not the main game.exe it self, same for KoToR BoPC.
That still doesn't answer my question. It's like saying you have a problem in your house, and when asked what the problem is, saying that it's a problem in your kitchen. If it's a graphics problem, you can bet that knowing what your graphics card is would help (i.e. what you have in the kitchen). Regardless, doing a search for "republic commando 3d analyze" on Google, the very first result should solve your problem, or at least eliminate a few options.