Fake Anti-virus cant remove

[Jacee]

I'd still insist on doing a wipe and install rather than scanning with some basic stuffs like MSE, Spysweeper.
You can never be sure how much damage the rootkit has done. They can install hooks at such low levels that can survive formats and scans. Moreover, they may also create hidden partitions or locations as you say, which acts as their backup and working area.
However, a wipe would very likely clean the remnants.

Yep, what EzioAuditore said!

 

[EzioAuditore]

Its not just about partitions, they may not create partition, but use any 'backward' portion of the HDD, (i'm not getting the right term for it now) invisible to the system. When you scan your pc, they replaces the infected files with the legit ones and thus can bypass scans very easily, providing a backdoor to it's author.
It's just as simple as 'Once you get infected by a rootkit, you can never ever be sure that the machine is clean.'
@Jacee
Thank you.