How to close an external programme after execution in Matlab

I have successfully called and executed an external programme in Matlab, the programme requires file input before running therefore I used the following commands:

A=system('C:\Zeek\ZEEKER.exe C:\Zeek\test1.DAT')
or 
! "C:\Zeek\ZEEKER.exe" C:\Zeek\test1.DAT

both of those commands worked fine and I can see the results file is stored in the same directory. However, the programme creates a window (please click ok to exit) that have to be clicked in order to close the programme and return back to Matlab. that means in every loop, I have to click ok to complete running the code. I have tried commands like (&) or (& exit&&) but did not work. please, is there an automated way to close the programme? Thanks in advance for your help

[Ahmed Abed]

Any help please! Thanks