To run ffmpeg commands in asp.net you need to use Media Handler class. Here is an example how to use media handler class to run ffmpeg commands.
//Create media handler object of Media_handler class
Media_handler mymediahandler=new Media_handler();
// Get web site application path
string webapppath =Server.MapPath(Request.ApplicationPath);
//Get ffmpeg.exe full path from mapping
string ffmpeg_path=HttpContext.Current.Server.MapPath(“ffmpeg.exe”);
//Run FFMPEG command by calling Execute_FFMPEG function of Media_handler class
mymediahandler.Execute_FFMPEG(ffmpeg_path, “-i c:\\clock.avi -vcodec mp3 c:\\clock.flv”);