How do you want to stop the external function? Is it possible to stop it in a regular way or do you have to kill the process in the hard way? The second method might leave some partially written output files and other junk on your computer.
You can start the external function using system('Program.exe &') and wait the wanted time. The exact procedure depends on how the external function can show, that it has finished and on your operating system. So please add more details in the body of your question - posting this as a comment is not optimal for the readers.