You shouldn't have any viruses/malware after you reinstall Windows. If you have viruses that are persisting after a reinstall, then either you have a rootkit or if you have an external HDD/flash drive/etc. that could be infected.
Oh. So no need to scan in safe mode after re-installing OS. I currently have an AVG 2014 anti-virus. I just want to make sure that my pc is not infected.