Windows 7 recovery virus (uninstall)?

So i've ran two macros in ms dos, one to terminate files in my c drive that generated virus popups (RKill) and another to restore hidden files (h+). After I ran my malwarebytes anti malware scan and deleted all infected objects.......BUTTT when i restarted my pc I had to do it all over again b/c the virus started all over again with the popups and hiding file. This second time around I did all steps besides restart pc....any suggestions??