Answer for:

Why some empty folders can't be deleted ?

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I tried various tools recommended here. Some tools like unlocker can remove the folders, but after reboot, then they come up again.
Seanferd was right when he mentioned that they are owned by window. I checked the process which is using those folders, and it is winlogon.exe.
Unless I can locate the initialization (file?) of winlogon.exe and remove the entry from the initialization, I think there is no way to remove it completely.