The 64bit version of Windows includes a 32bit emulator that allows 32bit software programs to install and run on the system.
The Program Files (x86) and Windows\SysWOW64 folders contain all of the 32bit versions of the system files that makes this possible.
The corresponding Program Files and Windows\System32 folders contain all of the 64bit versions of these same system files.
If you were successful in removing and of these these folders/files, you would completely corrupt the operating system which would require a reinstall.