G'day Ppeoc,

The general rule (not one that's written down, as far as I know, but rather something that's served me very well for many years) is to pass a reference to a variable then modify the dereferenced value within the GUI code.

Here's a quick & dirty example (no niceties like titles, geometry, colours, borders, etc.) to demonstrate this:

#!/usr/bin/env perl -l

use strict;
use warnings;

use Tk;

my $mw = MainWindow::->new();

my @choices = qw{A B C D};
my $chosen;
my $tl;

$mw->Button(-text => 'Make Choice', -command => sub {
    make_choice(\$mw, \$tl, \@choices, \$chosen);
})->pack();
$mw->Button(-text => 'Show Choice', -command => sub {
    if (defined $chosen) {
        print "You chose: $chosen";
    }
    else {
        print "Nothing chosen yet!";
    }
})->pack();
$mw->Button(-text => 'Exit', -command => sub { exit })->pack();

MainLoop;

sub make_choice {
    my ($parent, $tl, $choices, $chosen) = @_;

    if (! Exists($$tl)) {
        $$tl = $$parent->Toplevel();
        my $lb = $$tl->Scrolled('Listbox',
            -selectmode => 'single',
            -scrollbars => 'osoe',
        )->pack();
        $lb->insert(end => @$choices);

        $$tl->Button(-text => 'Done', -command => sub {
            my $selection = $lb->curselection();

            if (ref $selection) {
                $$chosen = $choices->[$selection->[0]];
            }

            $$tl->grabRelease();
            $$tl->withdraw();
        })->pack();
    }
    else {
        $$tl->deiconify();
        $$tl->raise();
    }

    $$tl->grab();
}
[download]

Note that the make_choice(...) call only has references as arguments; accordingly, sub make_choice {...} is totally independent of any global variables. You could call it with a completely different set of variables and, whatever equates to $chosen in the calling code is modified by $$chosen = ... in &make_choice: there's no need to return $chosen as it's already updated with the new value in the calling code.

As a quick example, clicking on "Show Choice", "Make Choice", "B", "Done", "Show Choice", "Exit" gives this output:

Nothing chosen yet!
You chose: B
[download]

Now, I wasn't entirely sure from your description, but I think you want your program to do some non-GUI stuff, then some GUI stuff, then more non-GUI stuff. I achieved that by keeping &make_choice as is and wrapping nearly everything before it in a subroutine (&run_gui) with these minor changes:

sub run_gui {
    my $choice = shift;
    ...
    ... sub { $mw->destroy } ... # instead of sub { exit }
    ...
    $$choice = $chosen;
}
[download]

And adding a call to run_gui(\$choice); (with a few print statements to indicate what's happening). Repeating the interaction shown in the earlier "quick example", gives this output:

Do something before GUI.
Hit <Enter> to start GUI: 

Nothing chosen yet!
You chose: B
Your choice: B
Do something after GUI.
[download]

Here's the new script in its entirety (in the spoiler):

You can probably gain a greater understanding of what's happening here by searching for "closure" in perlref and perlsub. Also, in case you haven't already seen it, take a look at Tk::callbacks.