How does one get that level of control over the CPU using C - considering that C is one of the lower level languages.
If you want to learn how to control a microprocessor (CPU) with C, buy a development board (like the PICdem board) and learn how to program a microprocessor in C-Language. You'll learn how to talk to registers, set up interrupts and all that fun stuff - You can even set up your own multi-threading paradigm.

I'm sure that everyone will agree that Changing/bypassing anything set up by your OS on your computer is asking for trouble.