for %%f in (*.mkv) DO ("%~dp0Tools\mkvtoolnix\mkvextract.exe"  tracks "%%f" 1:"%~dp0Output\%%~nf_Track1.h264" 2:"%~dp0Output\%%~nf_Track2.aac")

if not exist "%~dp0MP4" md "%~dp0MP4"

for %%f in (*.mkv) DO ("%~dp0Tools\Mp4Box\MP4Box.exe" -add "%~dp0Output\%%~nf_Track1.h264:lang=en:fps=25.000:sbr" -add "%~dp0Output\%%~nf_Track2.aac:lang=en:sbr" "%~dp0\MP4\%%~nf.mp4")

rd /s /q "%~dp0Output"