SBS2011 Windows directory permissions messed up by AV

I have a SBS2011 in production and about a week ago our Anti-Virus detected about 5000 infected files. It said it successfully cleaned those files and removed the threat but since then there's been some problems.
When I would log in with my normal Network Administrator Role user account and try to  execute any program I would get an error stating the "Digital Signature was invalid". I Logged in as the Built-in Administrator and ran SFC /scannow and
that appears to have resolved that problem.
However, when I browse into the Windows Directory I notice there are several hundred files in C:\Windows, C:Windows\System32, and C:\Windows\SysWOW64 that have a padlock Icon. When I examine the permissions on those files The Security Tab of the files Properties
says:
"No permissions have been assigned for this object.
Warning: this is a potential security risk because anyone who can access this object can take ownership of it. The object’s owner should assign permissions as soon as possible."
How can I reset the permissions on all of the .exe files within the C:\Windows directory back to what they should be?

Kidwon,
the command line tool is ICACLS.
https://technet.microsoft.com/en-us/library/cc753525.aspx
You may need first build a list of the files in question from a working win srv 2008 r2.
Jan

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