Pareing down the company table

I used to pair down the country table by editing inc/prof.inc.php - that is where the list of countries were.  After a recent upgrade, I noticed all those obscure countries came back, but when I went to edit this file found they were no longer there.  How do I pare down the country table now?  Can I do it directly in the predefined values table?  That is the way it should be, but it didn't work that way in previous versions.