Antivirus to fix the malware infected files (not to delete them)?

Question

My server got hit with malware. Now I downloaded full back up. When I scan it for a virus, my anti-virus deletes the infected files but I need them to be fixed and upload back. Please suggest me free anti-virus to fix the virus.

PS: There are 7000 infected files so there is no chance of fixing them one by one manually.