The objects are on the AnchorPane which will take the size of the window as definrd by #MainFormWidth and #MainFormHeight, you need to add a sub pane and move the objects to that (select the objects then choose arrange / Wrap in / Pane in the Scenebuilder menu). You will then be able to size and move the pane within the window. Unless that is all you want in the window, in which case you can size it using #MainFormWidth and #MainFormHeight.