[m0sa]

Hello, I'm sorry if the question seems a bit stupid but I need to know for sure whether the .exe files located in Windows/system/ directory (such as calc.exe, notepad.exe, etc) are all non-obfuscated or they have some kind of obfuscation or protection against reverse engineering.

Thanks

[EP_X0FF]

No, they don't, except EULA.

[r3shl4k1sh]

They aren't protected against Reverse Engineering.
But many of the DLLs have various protection against RCE (ASLR, Security Cookies and the like).