Rootkit malware dig themselves deeply into an operating system, so deeply in fact that removing them can be a major pain in the rear. If you have a system infected with the Trojan:Win32/Popureb.E then Microsoft is now recommending that users find their Windows recovery disc and use than to fix the MBR (Master Boot Record):
If your system does get infected with Trojan:Win32/Popureb.E, we advise you to fix the MBR and then use a recovery CD to restore your system to a pre-infected state (as sometimes restoring a system may not restore the MBR). To fix the MBR, we advise that you use the System Recovery Console, which supports a command called "fixmbr".
Rootkits/bootkits are a major pain in the rear to remove, and because they burrow themselves so deeply into the OS, and also create such a massive security vulnerability, the best thing to do might be to either recover the system from a clean backup or wipe the system and reinstall.
It's the only way to be sure that the malware is all gone.