A method, computer program product and system for restoring previously un-backed up data during a system restore. A computing system may include a locked partition in its storage medium to store an alternate operating system and backed-up files. The alternate operating system may determine which files have been modified since the most recent backup and run a virus scan on those modified files. The alternate operating system may copy the modified files with no detected viruses as well as those modified files with a detected virus but cleaned by the virus scan. The backup files in the locked partition that have been modified since the most recent backup operation may be replaced with these uncorrupted modified files. In this manner, the system may be able to recover files since the most recent backup while ensuring at least in part that the restored files do not contain any viruses.