Hi Advait,
We have multiple layers of technology built into the scanner (SVRT as well as normal SAV) that allows us to detect and cleanup rootkit infections whlist in the loaded operating system. In the event that a malware component cannot be cleaned immediately we schedule cleanup to be carried out on a reboot of the system - in this case a message is shown to the end user that a reboot is required.
So in short, you should find that SVRT and SAV are as effective as pre-boot scanning tools.
Regards,
Andy
P.S.
If you wish to run a scan that is completely indepent of the operating system I would recommend our other free tool, SBAV. Please be careful with it as if used incorrectly you could damage the machine.
http://www.sophos.com/en-us/support/knowledgebase/52053.aspx