I put a very good tutorial on dummying on
my site (in the tutorial page of the sorttxt section). You can even make these invisible if you want (use my tool in software section if not using a sort).
You wouldn't want to get rid of them, if anything, if you're going to repack a game you want to make the dummy as big as possible. In my guide you can find how to make it to the last sector.
Good luck... and yep, dummys are typically named 000*.DAT because that puts them first in the file system (most of the time). I recommend using 0.0 for your dummy name.