A single Perl/Tk app can create any number of "MainWindow" objects, and any number of "Toplevel" windows -- both are handled by the user's main window manager. (Check the corresponding man pages to see what's different and common among these two types of widgets.)

You can associate create, destroy, iconify and de-iconify (aka "unmap" and "map") operations with whatever user controls seem appropriate (buttons, menu options, etc), so that windows appear and disappear whenever the user decides; controlling geometry requires somewhat more attention to detail, but is certainly possible in unix/x-windows environment (I'm not sure about ms-windows, but it should work there as well).