By "pop up" I gather that you are opening a new window that you want to be "modal"-- the user must finish with and close that window before they are permitted to interact with any other FileMaker windows that may also be open.
In FileMaker 11 and earlier, this is often managed with a pause/resume step inside a loop. In FileMaker 12, this is no longer necessary as we can use Advanced Window Options to simply specify that the window be "modal".
New WIndow, go to layout and other steps first open a new window, select a layout for it and to size and position the window as desired the script then ends with these steps:
Allow User abort [off]
Note that this traps you in an infinite loop and that you cannot abort the script except by either force quitting FileMaker or using FileMaker Advanced's script debugger to abort the script and thus must be used and tested with care. To enable the user to close the window and abort this script, you use a button that either specifies "Halt script" in button setup or use a script that ends with the Halt Script script step.
If you have FileMaker Advanced, you can set up the window's layout with a custom menu where the close window menu option performs a script to close the window and halt the infinite loop with a Halt Script step. If set up correctly, that enables a user to close the window by clicking the close window control in the corner of the window.
Perfect thank you Phil, I have FMA 12 so I was able to simply switch it to "modal" and everything seems to be working just fine :)