Oops, I meant this:
vlc inputfile.mp4 --start-time 180 --stop-time 360 :sout=#transcode:std{access=file,acodec=mp4a,vcodec=mp4v,mux=mp4,url=outputfile.mp4} vlc:quit
This will transcode 3 minutes of the MP4 into MP4. It will also quit the program.