The problem is that the pop up window is almost certainly not a separate application (or process), but an integral part of the same application. If you were to detect the process id/handle for the task controlling the popup window and kill it, you would be killing the program that produces it, and your overall process would not complete correctly.

That leaves you with two options. Re-licence the application or write a program that 'clicks' the appropriate button on the popup window to cause it to be dismissed.

The former is probably the easiest solution and long term, the right one unless you can find an alternative to it that performs the same job.

The second, is more complicated, but could be done using perl. A good place to start would be Win32::CtrlGUI which will allow your script to look for the specific popup window, and then 'send' a keystroke or mouse click to it. However, working out how to determine which window to look for, and what and where to send the keystroke(s) or mouse clicks to is non-trivial and not something that anyone here could really help you with much unless they had a copy of the same application.

You'll need to read the documentation to the module quite carefully.