$ ffmpeg -i 1.mov -map_channel 0.1.0 -map_channel 0.1.1 -vn 1.mp4
ffmpeg version N-56979-g162e22e Copyright (c) 2000-2013 the FFmpeg developers
  built on Oct  8 2013 12:15:29 with llvm-gcc 4.2.1 (LLVM build 2336.11.00)
  configuration: --arch=x86_64 --enable-gpl --enable-version3 --enable-postproc --enable-libfdk-aac --enable-libfreetype --enable-libmp3lame --enable-libass --enable-libopenjpeg --enable-openssl --enable-libopus --enable-libschroedinger --enable-libspeex --enable-libtheora --enable-libvorbis --enable-libvpx --enable-libx264 --enable-yasm --enable-swscale --enable-avfilter --enable-libmodplug --enable-libbluray --enable-gnutls --enable-shared --enable-pthreads --enable-nonfree --enable-opencl --enable-avresample
  libavutil      52. 46.101 / 52. 46.101
  libavcodec     55. 35.100 / 55. 35.100
  libavformat    55. 19.100 / 55. 19.100
  libavdevice    55.  4.100 / 55.  4.100
  libavfilter     3. 88.101 /  3. 88.101
  libavresample   1.  1.  0 /  1.  1.  0
  libswscale      2.  5.101 /  2.  5.101
  libswresample   0. 17.103 /  0. 17.103
  libpostproc    52.  3.100 / 52.  3.100
Input #0, mov,mp4,m4a,3gp,3g2,mj2, from '1.mov':
  Metadata:
    creation_time   : 2013-10-16 19:41:13
  Duration: 00:00:49.84, start: 0.000000, bitrate: 172345 kb/s
    Stream #0:0(eng): Video: prores (apch / 0x68637061), yuv422p10le, 1920x1080, 168885 kb/s, SAR 1:1 DAR 16:9, 23.98 fps, 23.98 tbr, 24k tbn, 24k tbc (default)
    Metadata:
      creation_time   : 2013-10-16 19:41:13
      handler_name    : Apple Alias Data Handler
      timecode        : 09:47:53:20
    Stream #0:1(eng): Audio: pcm_s24le (lpcm / 0x6D63706C), 48000 Hz, 3.0, s32, 3456 kb/s (default)
    Metadata:
      creation_time   : 2013-10-16 19:41:13
      handler_name    : Apple Alias Data Handler
    Stream #0:2(eng): Data: none (tmcd / 0x64636D74) (default)
    Metadata:
      creation_time   : 2013-10-16 19:42:07
      handler_name    : Apple Alias Data Handler
      timecode        : 09:47:53:20
File '1.mp4' already exists. Overwrite ? [y/N] y
-map_channel is forwarded to lavfi similarly to -af pan=0x3:c0=c0:c1=c1.
[pan @ 0x7ff18a000940] This syntax is deprecated. Use '|' to separate the list items.
[pan @ 0x7ff18a000940] Pure channel mapping detected: 0 1
Output #0, mp4, to '1.mp4':
  Metadata:
    encoder         : Lavf55.19.100
    Stream #0:0(eng): Audio: aac (libfdk_aac) ([64][0][0][0] / 0x0040), 48000 Hz, stereo, s16, 139 kb/s (default)
    Metadata:
      creation_time   : 2013-10-16 19:41:13
      handler_name    : Apple Alias Data Handler
Stream mapping:
  Stream #0:1 -> #0:0 (pcm_s24le -> libfdk_aac)
Press [q] to stop, [?] for help
size=     860kB time=00:00:49.85 bitrate= 141.4kbits/s
video:0kB audio:851kB subtitle:0 global headers:0kB muxing overhead 1.160101%