How to close a popup dialog?

Looking at the Scenebuilder1.1 Login sample, a new scene is created which is placed on stage.
How would such a popup get closed and get back the original main screen?
    private Initializable replaceSceneContent(String fxml) throws Exception {
        FXMLLoader loader = new FXMLLoader();
        InputStream in = Main.class.getResourceAsStream(fxml);
        loader.setBuilderFactory(new JavaFXBuilderFactory());
        loader.setLocation(Main.class.getResource(fxml));
        AnchorPane page;
        try {
            page = (AnchorPane) loader.load(in);
        } finally {
            in.close();
        // store the stage height in case the user has resized the window
        double stageWidth = stage.getWidth();
        if (!Double.isNaN(stageWidth)) {
            stageWidth -= (stage.getWidth() - stage.getScene().getWidth());
        double stageHeight = stage.getHeight();
        if (!Double.isNaN(stageHeight)) {
            stageHeight -= (stage.getHeight() - stage.getScene().getHeight());
        Scene scene = new Scene(page);
        if (!Double.isNaN(stageWidth)) {
            page.setPrefWidth(stageWidth);
        if (!Double.isNaN(stageHeight)) {
            page.setPrefHeight(stageHeight);
        stage.setScene(scene);
        stage.sizeToScene();
        return (Initializable) loader.getController();
    }

Thanks for your reply. I rewrote the sample to do this - created a new Stage, and it worked. :)
    <T extends ControllerBase> T replaceSceneContent(T controller, String fxml, String message) {
        try {
            AnchorPane page;
            FXMLLoader loader = new FXMLLoader(getClass().getResource(fxml));
            page = (AnchorPane) loader.load();
            Stage dialog = new Stage(StageStyle.UTILITY);
            dialog.initOwner(MainPane.primaryStage);
            dialog.getIcons().add(new Image("/resources/my-icon.gif"));
            dialog.initModality(Modality.WINDOW_MODAL);
            Scene scene = new Scene(page);
            dialog.setScene(scene);
            T c = loader.getController();
            c.stage = dialog;
            c.setMessage(message);
            dialog.showAndWait();
            return c;
        } catch (IOException ex) {
            Logger.getLogger(main_screenController.class.getName()).log(Level.SEVERE, null, ex);
        return null;
    }

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