system() runs a command thru the currently configured shell. In Windows, that means cmd.exe. So if you want to see what the command does, run cmd.exe then type cls. It's the DOS/Windows command for clearing the screen (it came from BASIC).
fflush() flushes a file's buffer to disk. When you work with files (using FILE*), you're dealing with a buffered file. It's buffered to improve performance. But sometimes you want to update the physical file with what's been buffered, it's called flushing the buffer. fflush does that.