Run ffmpeg twice , each time specify that just 1 track be copy to output.
Example on diff mp4 will provide most of the idea which u will need to adapt to your specific track types for the respective video/audio in your container...
MP4 example : demux h264 and aac tracks to separate outputs (tout1, tout2 )
Whats in input?
Input #0, mov,mp4,m4a,3gp,3g2,mj2, from 'phoneCam_20120902_112701.mp4':
Metadata:
major_brand : isom
minor_version : 0
compatible_brands: isom3gp4
creation_time : 2012-09-02 18:27:14
Duration: 00:00:12.65, start: 0.000000, bitrate: 8011 kb/s
Stream #0:0(eng): Video: h264 (Baseline) (avc1 / 0x31637661), yuv420p, 1280x720, 7707 kb/s, SAR 65536:65536 DAR 16:9, 28.64 fps, 29.83 tbr, 90k tbn, 180k tbc
Metadata:
creation_time : 2012-09-02 18:27:14
handler_name : VideoHandle
Stream #0:1(eng): Audio: aac (mp4a / 0x6134706D), 48000 Hz, mono, s16, 96 kb/s
Pass 1, just get the Vid
ffmpeg -i phoneCam_20120902_112701.mp4 -map 0:0 -c copy tout1.mp4
Pass2 just get the aud
ffmpeg -i phoneCam_20120902_112701.mp4 -map 0:1 -c aac -ar 48000 -ab
48000 -strict -2 tout2.3gp
In your program, just run ffmpeg from the CLI or call main() in ffmpeg.c