How did you remove LW? If you did it through add/remove programs, that can cause problems. Use your computer's search to look for all files & folders with LimeWire in the name & delete from there.

Before you uninstalled LW, was it popping up all the time & refusing to stay closed? If that was happening, you probably have a worm. In that case, uninstalling LW isn't going to get rid of it...you'll just keep getting other popups. If that was your problem, try the fix here. It's worked for a lot of people.
The easy fix for Limewire popping up every few seconds (try this first)

If that wasn't your problem to start with, just ignore what I said