A parallel installation is the best primary tool to use in disinfecting malware infestations. The first benefit is that the malware, in most cases, is not active when the primary Windows installation is not loaded. Most malware aimed at Windows makes clever and devious use of the Windows API's to perfrom its tasks, but many of those same Windows API's are necessary for anti-malware tools to use in combating the malware. This is why some anti-malware tools cannot even be installed on an infected system. Use of the API's and/or registry settings is being blocked by the malware.
When using a parallel installation in the battle against malware, it's very important to get the parallel installation completely updated with all patches and security updates. Anti-malware tools can then be installed on the parallel installation, and those tools also need to have the latest available updates.
In a parallel installation, your anti-malware tools have the capability of inspecting the entire system and doing their work unencumbered by the malware. In a parallel installation, the Windows API's are available to the anti-malware tools installed on the parallel installation, but not usually available to the malware on the Primary Windows installation, since neither the malware nor the Windows API's of the primary installation are booted up nor running.
The entire machine, all hard drives and partitions can be scanned and in most cases cleaned by the anti-malware tools running on the parallel installation. Once the machine has been thoroughly cleaned from the relative safety of the parallel installation, the system can be rebooted into the primary Windows installation and the entire system scanned again with all the anti-malware tools to verify that malware removal is indeed complete.