Unhide.exe will unhide (attrib -H) all files on any fixed disks that are present after an infection and cleaning has left them hidden and invisible. Unhide is indiscriminate and it will make all files visible with attrib -H. This includes all files hidden by the malware as well as those which are normally hidden by the operating system or hidden by the user.
Only files that are +S (system) will not have their hidden attribute removed by unhide.exe. This is because the majority of legitimate Windows files that are hidden are also +S. For example, Desktop.ini is a system file and the tool is designed not to remove hidden attribute for system files.
There is no way to effectively whitelist the files that need to be hidden normally as they are different for every computer. The attrib -H change which makes file visible is reversible for normally hidden files. To hide the files in Windows, you can reverse the steps provided in How to see hidden files in Windows
. For other files not governed by Windows Folder Options you will have to manually rehide them. To do that, right-click on the file, choose properties and check the Attributes box next to Hidden.