Some malicious software will edit the Windows registry to prevent showing of hidden files and folders. Normally, this is to prevent the user from discovering the presence of said malicious software.
After removal of the malware, antivirus tools do not perform registry cleanups like these since it's entirely valid that a system administrator might have enforced certain restrictions on the system to prevent users from screwing up the system.
In such cases, simply run regedit and browse to HKLM\SOFTWARE\Microsoft\Windows\CurrentVersion\Explorer\Advanced\Folder\Hidden and ensure that the key SHOWALL is of type REG_DWORD and change the value from 0 to 1. The "Show hidden files and folders" option in Folder Options should now be working again.
Show Hidden File and Folders Not Working?