Removing Viruses Manually. 1  1. Download Autoruns. 2  2. Adjust Autoruns' options. 3  3. Reboot into Safe Mode with Networking.  4. Start the Autoruns 1  program. 5. Begin searching for suspicious entries.  6. Delete the first malware-related 1  entry. 7. Remove the files associated with the deleted 2  entry. 8. Reboot your computer normally.