chdir works, and I'd suggest that as well. But there's also the problem in your system call of backslashes and quotes. Specifically, you need to do one of three things -- change the quoted stuff to "cd /d c:\\MyNewWorkingDir" or 'cd /d c:\MyNewWorkingDir' (note the single quotes) or "cd /d c:/MyNewWorkingDir"

Note that I don't think this will solve your problems, as noted in other replies. But any other system calls will need to have the \ working properly...