How to achieve the following structure in javafx?

JFXPanel is for embedding JavaFX scenes inside a Swing application, which doesn't sound like what your are doing, so a JFXPanel is probably the wrong component type to use for your application.

I guess (and I could be wrong) that your application is a JavaFX application in which you would like to embed a Swing component - in which case you use a SwingNode.

JavaFX scene
 - JavaFX layout pane root
   - JavaFX ScrollPane 
     - SwingNode 
       - Swing component

In general, mixing JavaFX and Swing is not usually recommended.

I note that your question is tagged javafx-2, so note that SwingNode only exists from Java 8 on; i.e., it does not exist in Java 7, so there is no way to accomplish the structure you outline in your question within the context of Java 7 or JavaFX 2.2.