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Never delete System32 considering without those files your computer will never reboot again and it will legitimately die. If you have a virus, let and antivirus software take care of it. Never remove ANY system32 files. It will screw up your whole computer.
Linux does not contain anything called "System32" by default. You would remove a file called System32 by entering rm System32. You would remove a directory called System32 by entering rm -r System32.
DO NOT DELETE IT. your copy of windows will "break", and you will have to reinstall windows.