I think you are running into difficulties because you don't have a decent data structure setup to hold the selections. You have a hodgepodge of local and global hashes and variables which are cumbersome to collect and sort. You might be better off reorganizing your data into a better hash which you can more easily loop thru.

Furthermore you did not use strict and use warnings as I mentioned to you before in Re^3: Optionmenu Variable in Name. This programming negligence of yours causes us to have to track down all sorts of bugs in your code. Same thing again here. If you add strict and warnings, you get

Global symbol "%mat_lab" requires explicit package name at ./959204.pl
+ line 41.
Global symbol "%mat_lab" requires explicit package name at ./959204.pl
+ line 43.
Global symbol "%mat" requires explicit package name at ./959204.pl lin
+e 66.
Global symbol "%t" requires explicit package name at ./959204.pl line 
+80.
Global symbol "%ort" requires explicit package name at ./959204.pl lin
+e 94.
Execution of ./959204.pl aborted due to compilation errors.
[download]

This is important, because you treat %t, %ort, and %mat like they are globals but they are NOT. So how can you access them in your sub print_input_file?

A fixed version of your code shows how to get that sub to print your values.

#!/usr/bin/perl
use warnings;
use strict;
use Tk;
use Cwd;

######################################################################
+#####################
# GUI Building 
######################################################################
+#####################

# make the selections available to the print_input_values sub
my %t;
my %mat;
my %ort;
my %mat_lab;


# Create Main Window
my $mw = new MainWindow;
my $lam_num;
my $row=1;
my $column=1;
my $lam_mat_frm = $mw -> Frame();
$lam_mat_frm->grid(-row=>$row, -column=>$column,-columnspan=>6);
my $lam_num_lab = $lam_mat_frm -> Label(-text=>"Input the number of pl
+ies in the laminate.",
    -font=>"ansi 10 bold");
$lam_num_lab->grid(-row=>$row, -column=>$column);
$column++;
my $lam_num_ent = $lam_mat_frm -> Entry(-textvariable=> \$lam_num);
$lam_num_ent->grid(-row=>$row, -column=>$column);
$column++;
my $lam_data_button = $lam_mat_frm->Button(-text=>"Input Laminate Data
+",
    -command=> \&input_lam_data);
$lam_data_button->grid(-row=>$row, -column=>$column);

MainLoop;

sub input_lam_data {
    $row=4;
    $column=2;
    my @lam_mat_t_lab = (
    'Material',
    'Thickness',
    'Orientation',
    );
    my $n = 1;
    for my $label (@lam_mat_t_lab) {
        $mat_lab{$n} = $lam_mat_frm -> Label (-text=> $label,
        -font=>"ansi 8 bold");
        $mat_lab{$n}->grid(-row=>$row, -column=>$column);
        $column=$column+1;
    };
    my %ply_lab;
    $n = 1;
    $row=5;
    do {
        $column = 1;
        $ply_lab{$n} = $lam_mat_frm -> Label (-text=>"Ply $n",
        -font=>"ansi 8 bold");
        $ply_lab{$n}->grid(-row=>$row,-column=>$column);
        $row = $row+1;
        $n = $n+1;
    } until ($n == $lam_num+1);

    # Create Material Optionmenus
    my @mats = ("PW","8HS","Tape");
    my %mat_optmen;
    $n = 1;
    $row=5;
    $column=2;
    do {
        $mat_optmen{$n} = $lam_mat_frm -> Optionmenu(-options => \@mat
+s,
        -variable => \$mat{$n});
        $mat_optmen{$n}->grid(-row=>$row,-column=>$column);
        $row=$row+1;
        $n = $n + 1;
    } until ($n == $lam_num+1);
    
    # Create Thickness Optionmenus
    my @ts = ("0.0077","0.0147","0.0054");
    my %t_optmen;
    $n = 1;
    $row=5;
    $column=3;
    do {
        $t_optmen{$n} = $lam_mat_frm -> Optionmenu(-options => \@ts,
        -variable => \$t{$n});
        $t_optmen{$n}->grid(-row=>$row,-column=>$column);
        $row=$row+1;
        $n = $n + 1;
    } until ($n == $lam_num+1);

    # Create Orientation Optionmenus
    my @orts = ("-45","0","45","90");
    my %ort_optmen;
    $n = 1;
    $row=5;
    $column=4;
    do {
        $ort_optmen{$n} = $lam_mat_frm -> Optionmenu(-options => \@ort
+s,
        -variable => \$ort{$n});
        $ort_optmen{$n}->grid(-row=>$row,-column=>$column);
        $row=$row+1;
        $n = $n + 1;
    } until ($n == $lam_num+1);
    my $print_button = $lam_mat_frm->Button(-text=>"Print BJSFM Input 
+File",
    -command=> \&print_input_file);
    $print_button->grid(-row=>$row,-column=>1);
}

sub print_input_file {
 print "$lam_num\n";

 my @values;

foreach my $n (1.. ($lam_num) ){
    push @values, $mat{$n};
    push @values, $t{$n};
    push @values, $ort{$n};
    
   }

print  join ",", @values,"\n";
}
[download]