My father and my uncle were grain farmers. They had a very effective strategy for ridding their fields of weeds: plant alternating crops or summer-fallow. Thus the weeds were either exposed to cultivation or not always in their preferred niche.
Malware is software in a niche. It cannot be too open or folks will just kill the process. Instead malware has become like weeds growing in cracks where other software cannot see it. The ultimate is the rootkit where even the host OS cannot see the malware. InfosecInstitute has a nice piece detailing the extent to which the rootkit, ZeroAccess, burrows into that other OS.
“This rootkit has low level disk access that allows it to create new volumes that are totally hidden from the victimâ€™s operating system and Antivirus. Consider the case where someone attempts to remove the rootkit by formatting the volume where their OS is installed (say the c:\) and reinstalling Windows. ZeroAccess will survive this cleaning process and reinstall itself onto the fresh copy of Windows. This is likely very frustrating for anyone attacked by ZeroAccess.”
Amen. Then, along comes GNU/Linux not knowing anything about that other OS’ volume structure and overwrites the whole thing with wholesome Free Software. Just as a farmer gains leverage on the weeds by alternating the environment, M$ and its customers could ensure greater freedom from malware by installing GNU/Linux alternately with that other OS. The malware burrowed into the hard drive would be flushed by GNU/Linux, making the world a better place.
Don’t re-install that other OS. Pave it over with GNU/Linux and be free of malware. I recommend OEMs distribute GNU/Linux installation CDs with their machines to improve customer satisfaction.