I've been using this to convert the first audio track to AC3:
ffmpeg -i FILE.mkv -map 0:v -map 0:a:0 -map 0:s -c copy -c:a ac3 -b:a 640k FILE-AC3.mkv
And it has been working great.
I wanted to know what to add or change if I wanted a resulting file with nothing else except the video and the converted audio (and removes all subtitles, tags, global tags, chapters, etc.)
Thanks in advance.