Heeter, if you don't disable System File Protection, then yes, you can perform much of this in safemode. Some folders will return, though, upon restarting, but most will be empty.
If you download the free trial of XPLite, it can very simply, with one click, disable System File protection for you.
System File Protection is a joke anyway. I run with it disabled.
Microsoft should be concentrating on the protection of, and corruption of, and accidental deletion of, important system files...especially those files like the Hall.dll or pci.sys amoung others...which will prevent a good reboot of your system, and prevent Windows from opening. Instead, they choose to protect the "Tour" folder and such.