Well, to get the audio out you can use XMedia Recode to convert it to a WAV file for processing in Cubase.
To replace the original audio with the processed audio used to be easy in Cubase but that function was removed some time ago. I stopped trying to do this in Cubase and now use Vegas for this instead. Even the very cheap MAGIX Vegas Movie Studio will do this easily, but there are plenty of other free and open-source applications out there.