You probably want to use Tk::Wizard, see http://search.cpan.org/dist/Tk-Wizard/MANIFEST, Confused by variable scope in Tk::Wizard (hello closures) , Re: Confused by variable scope in Tk::Wizard (hello closures)

But if you want to stick with MainLoop you could write that like this (all lexically scoped and not-memory leaking )

#!/usr/bin/perl --
# Test to enter select directory with gui
# 
# 
# 
# 
# perltidy -olq  -csc -csci=10 -cscl="sub : BEGIN END if " -otr -opr -
+ce -nibc -i=4 -pt=0   "-nsak=*"
#!/usr/bin/perl --
use strict;
use warnings;

use Encode;
use Tk;

use Path::Class;
use Devel::CheckOS qw/ os_is /;

Main( @ARGV );
exit( 0 );

sub Main {
    &wadebug;
    
    my $initialdir = shift || 'Z:\Projects\RunMSMS\MGF\human\ion_trap'
+;
    my $end_file   = shift || 'Z:\Projects\RunMSMS\MGF\human\ion_trap\
+test_gui_output.txt';
    my $tissue     = shift || "plasma";
    
    tkgui( $initialdir, $end_file, $tissue );
}

sub tkgui {
    &wadebug;
    
    my( $initialdir, $end_file, $tissue ) = @_;
    my $mw         = Tk::MainWindow->new;
    my $tissue_but = $mw->Button(
        -text => 'Tissue Type',
        -command =>  [ \&select_tissue, $mw, $initialdir, \$tissue, ],
    );
    $tissue_but->grid( -row => 3, -column => 1 );

    $mw->Button(
        -text => 'Data Entry Complete',
        -command => [ \&do_end, $mw, $end_file, \$tissue, ],
    )->grid( -row => 10, -column => 1 );
    
    Tk::MainLoop();
}

sub select_tissue {
    &wadebug;
    
    my( $mw, $initialdir, $choiceref ) = @_;
    my $dir = $mw->chooseDirectory( -initialdir =>  $initialdir );
    
    if( os_is(qw( MicrosoftWindows )) ){
        $dir = encode( "windows-1252", $dir );
    }
    if( defined $dir and length $dir ){
        $dir = dir( $dir )->basename;
        if( length $dir ){
            $$choiceref = $dir;
        }
    }
    return;
}

sub do_end {
    use autodie qw/ open close /; ## make open(...) or die(...) automa
+tic
    
    &wadebug;
    
    my( $mw, $outfile, $tissueref ) = @_;
    
    print join " ", tissue => $$tissueref , "\n";
    
#    open my($FOUT),  '>>', $outfile;
#    print $FOUT "$$tissue\n";
#    close $FOUT;
    
    $mw->destroy; ## exit mainloop
}

sub wadebug {
    my( $package, $filename, $line, $subroutine, $hasargs ) = caller( 
+1 );
    for my $var ( @_ ){
        if( not ref $var ){
            use Data::Dump ();;
            print STDERR "# $line:$subroutine: @{[ Data::Dump::pp( $va
+r ) ]}\n";
        } elsif( ref($var) and ref($var) =~ m{ SCALAR | ARRAY | HASH }
+x ) {
            print STDERR "# $line:$subroutine: @{[ Data::Dump::pp( $va
+r ) ]}\n";
        } else {
            print STDERR "# $line:$subroutine: $var\n";
        }
    }
    print STDERR "\n";
}
__END__

# 28:main::tkgui: "Z:\\Projects\\RunMSMS\\MGF\\human\\ion_trap"
# 28:main::tkgui: "Z:\\Projects\\RunMSMS\\MGF\\human\\ion_trap\\test_g
+ui_output.txt"
# 28:main::tkgui: "plasma"

# 251:main::select_tissue: Tk::MainWindow=HASH(0x9a1804)
# 251:main::select_tissue: "Z:\\Projects\\RunMSMS\\MGF\\human\\ion_tra
+p"
# 251:main::select_tissue: \"plasma"

# 251:main::do_end: Tk::MainWindow=HASH(0x9a1804)
# 251:main::do_end: "Z:\\Projects\\RunMSMS\\MGF\\human\\ion_trap\\test
+_gui_output.txt"
# 251:main::do_end: \"x64"

tissue x64
[download]