Well, you can iconise the MainWindow, or in Tk speak - iconify.

Although I don't have the documentation handy, the MainWindow is merely a special case of a "Toplevel" widget. Special in that it is displayed automatically when you call MainLoop. It is displayed automatically, but every other "Toplevel" must be spcifically placed using one or another of the geometry managers. Thus having created your MainWindow you should then be able to call the iconfy method:

$mw->iconify();
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and have the pesky window disappear. To get it back?

$mw->deiconify();
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However it may not reappear on the top of the other windows, to ensure this use the raise method:

$mw->raise();
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jdtoronto