The easiest way to switch MKV to MP4, is to copy the existing video and audio streams and place into a new container. This avoids any encoding and hence no quality will be lost.
ffmpeg -i example.mkv -c copy example.mp4
If you want to batch convert multiple MKV files, you can switch into the directory and run the following:
for i in *mkv; do ffmpeg -i "$i" -c copy "${i%.mkv}.mp4"; done
for %i IN (*.mkv) DO ffmpeg -i "%i" -c copy "%i.mp4"