Compacting only deletes messages that you have previously clicked to delete, freeing up space in the folder.

David, Thanks for your speedy reply. A bit confused how you deliberately "delete messages that you have previously clicked to delete"? That's sorta why I want to do this. I want some but not all messages; mostly from friends or businesses. Thanks

In mbox files, a deleted message remains, but is marked for delete. That means that it still is taking up space on your computer but is not accessible. As deleted messages increase, this increases the size of the folder. The process of compacting is removing the 'dead' messages from the folder. This is just basic disc space maintenance.