-map -0:v:1
----
===== Example - remove the second audio stream =====
-map -0:a:1
----
===== Example - remove the second subtitle stream =====
-map -0:s:1
ffmpeg -i "input.mkv" -map 0 -map -0:v:1 -map -0:a:1 -map -0:s:1 -c copy "output.mkv"