The C language has no inherent concept of a display screen so if you need to "clear" your display start learning a GUI package. http://cplusplus.com/forum/beginner/1988/EDIT: oop, wrong link, see Moschops post below...
Ive heard that people can replace the "CLS" command with something malicious.
Anything you ever do with the system function is rolling the dice and hoping that nobody has put something malicious in place. Here's the local article on screen clearing: http://www.cplusplus.com/articles/4z18T05o/