You can't encrypt system files. Since they will be encrypted with your <current> account, the system files will be inaccessible to any other account, including administrator, Local Service, etc. Making the computer entirely unbootable.
Additionally, what are you trying to protect? What does encrypting, say, shell32.dll give you? Nothing. it makes the text green.
Encryption is about protecting secrets. encrypting a file that millions of other people have isn't protecting anything. It's utterly pointless.