I think you can create a Group with a scene that contain the value from the main window then use the getContent.add() method of Popup.
Group root = new Group();
Scene scene = new Scene(root,200,200);
//add the value form main windown to scene
Popup pop = new Popup();
Glad if this can help you
Thanks for your response.
I found out that we can use setUserData() and getUserData() in Node class to pass data between windows. The only problem I have is I'm using FXML for popup dialog so the Scene of my popup in the initialize funtion is always null.