How to arrange the layout of frames with navigation bar

You have canvas in mainFrame but you add NavigationToolbar to root

Use mainFrame in place of root in

toolbar = NavigationToolbar2TkAgg(canvas, mainFrame)

and you get button Close below NavigationToolbar

To get NavigationToolbar above canvas use

toolbar.pack(side=Tk.TOP)

EDIT: as for Tree - do you need this on left of NavigationToolbar and buttonFrame or below NavigationToolbar and above buttonFrame ?

As for me - it is easer to do it all with .grid(row=...,column=...) then with .pack()

CodeHunter