use Time::HiRes qw(time);

my $progress;
my $popup = Tk->after( 2, sub { $progress = create_progress_dialog } );

my $last_poll = time();
while (<$input_file>) {
    # let Tk process its events every 0.1 seconds:
    if (time - $last_poll > 0.1) {
        Tk->process_one_event();
    };
    ...
};

if ($progress) {
    undef $progress;
};
undef $popup; # cancel our Tk->after() timeout