In your subroutine, get_sub_dirs, you were missing this line:

@files = map { decode( 'utf8', "$dir/".$_ ) } sort @files;
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Now for your cancel button:

my $showbutton2 = $mw->Button(
    -text => 'Cancel',
    -bg   => 'red',
    -command => sub {exit} )->pack;

MainLoop();
[download]

Here's the complete script:

#!/usr/bin/perl

use strict;
use warnings;
use Tk;
use Tk::Pane;
use Encode;

my $topdir = '/root/Desktop';
my(@subdirs) = get_sub_dirs($topdir);

my $mw = tkinit();
$mw->geometry('200x400+200+200');

my $sp = $mw->Scrolled('Pane', 
    -scrollbars => 'osoe', 
    -sticky => 'nwse')->pack(
    -expand=>1, 
    -fill=>'both' 
);

my @cbvalues;
my @cbnames;
my $count = 0;
foreach my $d( @subdirs){
    $cbnames[$count] = $d;
    $sp->Checkbutton(-text => $d,
         -font=>[arial => 12],
         -onvalue => 1,
         -offvalue => 0,
         -variable => \$cbvalues[$count],
         -font => 'small',
         -bg => 'White',
     )->pack(-anchor=>'w')->pack();

$count++;
}

my $showbutton1 = $mw->Button(
    -text => 'OK',
    -bg   => 'green',
    -command => sub {
        my @selected = ();
        foreach my $c( 0.. $count ){
            if ( $cbvalues[$c] ){
                push @selected, $cbnames[$c];
        }
}

open (MYFILE, '>>', '/root/Desktop/System.pm');
print MYFILE "@selected\n";
close (MYFILE);
print "@selected\n";
})->pack();

my $showbutton2 = $mw->Button(
    -text => 'Cancel',
    -bg   => 'red',
    -command => sub {exit} )->pack;

MainLoop();


sub get_sub_dirs {
    my ($dir) = @_;
    opendir my $dh, $dir or die "Error: $!";
 
    my @files = grep !/^\.\.?$/, readdir $dh;
    closedir $dh;
    @files = map { decode( 'utf8', "$dir/".$_ ) } sort @files;
 
    my @sdirs;
    for my $file ( @files ) {
    if(!-f $file){push @sdirs,$file;}
    }
    return @sdirs;
}
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