Is it in the Windows version because I can't figure out how to do this with the Mac version. If it is possible I'd like to know as that would have helped me greatly in the past.
EDIT :
Just checked the output formats from Handbrake's site and I don't see how the OP could use it for his needs
Outputs:
File format: MP4 and MKV
Video: MPEG-4, H.264, or Theora
Audio: AAC, CoreAudio AAC (OS X Only), MP3, or Vorbis. AC-3 pass-through, DTS pass-thorugh (MKV only)