If you use Auto Update, then most likely you are using the Microsoft Malicious Software Removal Tool as well. So far I don't think it does do a lot of good to your system.
Considering that Microsoft updates the tool every month, I think Microsoft is a lot of steps behind the malicious software. I mean I don't want to wait for the tool to know the new malicious software (that are create oh so often) for one month. It's hopeless, because most of the damage might have been done already...
It's not really a 'excellent tool' because malware is always one step ahead of MS and anti-virus companies, but it doesn't hurt to try it... who knows? May be the tool might find something in your computer.