Okay, what you have to do is this:
Have your first GUI start a second copy of MATLAB to run the function that has to be interrupted. Set up anything necessary for the original MATLAB and the second MATLAB to communicate back and forth. Have the stop button be present in the original MATLAB, not the one running the function. When the stop button is detected in the first MATLAB, have the first MATLAB session kill the process that the function is running in. On MS Window, this would involve using system() to invoke "taskkill"; on OS-X or Linux, this would involve using system() to invoke "kill".
If you do not wish to create a second MATLAB session and kill the process like this, then there is no way to do what you want. MATLAB does not permit functions to be interrupted against their will. The methods for interrupting for loops and while loops are with the cooperation of the loop, with the loop checking from time to time whether it is being asked to be interrupted.
Ah, I just thought of another possibility. If you have the Parallel Computing Toolbox, then instead of starting a new MATLAB session, you can use parfeval() to run the function that needs to be interruptible. Then, when the button press is detected, you can issue a cancel() against the "future" that was returned by parfeval().
