In place of exit;, try $tk_win->destroy;.

#!/Perl/bin/perl -w
use strict;
use Tk;
my $filename;    
my $tk_win = MainWindow->new;
my $name_entry = $tk_win->Entry->pack;
$tk_win->Button(-text=>'Prepare It!',
        -command=>\&getFilename)->pack;
MainLoop;
print "Outside the MainLoop now!\n";
print "filename is $filename\n";

sub getFilename {
    $filename = $name_entry->get;
    $tk_win->destroy;
}
[download]