You need to use a file manager that can be used as root. You're going to be modifying files in /system, so it also needs to be able to remount /system as rw. Root explorer can definitely do it (that's the point), I think Estrongs can, but I recall it being buggy, and I'm not sure about Astro. I know it didn't used, but I'm not sure if that functionality was added.
Also, keep in mind that this method is not quite the same as what Launcherpro or the like would do. The launcher method just hides the icon. It's still has the ability to run in the background, and you can even add an icon for whatever is hidden back to the desktop. By renaming the apks, you're effectively uninstalling them. What that means is, make sure whatever you remove will not break something. Hiding icons with Launcherpro is harmless. Renaming apks can break things if you're removing something you shouldn't be. You can see the list of safe apks to remove in the Rooting for Dummies guide.
On that note, another way you can do this is with the terminal emulator. It's a pain to type commands on the phone, but if you have sshd or adb set up to use as a shell, I can give you the commands that actually make this a little faster.
