In general, you will want to get the book "Mastering Perl/Tk".

When you create the new window, you'll have a 'close' button or menu entry on it. If you have to create this (e.g. there sin't a module that will do this automagically), then you'll need to give this button a callback containing something that will reference the window. In this case, use a closure in the callback to hold the window object for use in destroy():

#!/usr/bin/perl -w
use Tk;

my $mw = MainWindow->new(-title=>"Demo");

my $HlpBttn = $mw->Button(-text=>"NEW",
                       -command=> sub { make_win(); });
$HlpBttn->pack();

MainLoop;

sub make_win 
{
    my $win = $mw->Toplevel(-title=>'new window',
                               -height=>10, -width=>50);

    my $Bttn = $win->Button(-text=>"CLOSE",
                       -command=> sub { close_win($win); }
                   )->pack; 
}

sub close_win
{
    my $thiswin = $_[0];
    $thiswin->destroy;
}
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The callback in each window has it's own instance of $win locked up in the coderef, ( -command => sub { close_win($win) } ), which retains the value $win had at the timew the window was created, so it "knows" which window to destroy when called. This coderef carrying around an instance of a lexical variable from the coderef's enclosing scope is called a "closure".

Update: Created a minimal example, got rid of all the old stuff.

--Bob Niederman, http://bob-n.com