Suna,
When creating a remote front panel, the red abort button should be available. If the abort button does not work, you can also change the "Disable VI" and "Safe Mode" dip switches to on and reboot the controller. When the FP-2000 reboots, the startup VI will not be running and you should be able to remove the exe. Before creating an executable, I would definitely recommend testing your front panel as a downloaded VI. If the stop button works in this mode, then it should also work in an embedded executable.
Regards,
Michael Shasteen
Applications Engineering
National Instruments
www.ni.com/ask