So to convert an MKV file to MP4:

Run "VLC media player".

From main menu select "Media" > "Convert / Save...".
On "File" tab, click "Add..." button.
Choose you MKV file. After that, it should be added to the list. (Alternatively,
you can drag&drop a file into the list.)
Click "Convert/Save" button.
Select Profile: "Video - H.264 + MP3 (MP4)".
Click on the icon button that has hint: "Edit selected profile".
On "Encapsulation" tab, leave "MP4/MOV" selected.
On "Video codec" tab, check both "Video" and "Keep original video track".
On "Audio codec" tab, similarly select both "Audio" and "Keep original audio
track".
Click "Save" button.
In "Destination" selection, click "Browse" button to select directory and file name
for you destination MP4 file.
Click "Start" button.
Observe progress bar in the main window as file is converted.
After that, my VLC (version 2.2.1) seems to hang in an infinite loop so I have to
kill it using system "Task Manager", but it doesn't matter - the destination file
is already created.