This is the code I have written, Many of the variables are not being used yet.

#!/usr/bin/perl

use strict;
use warnings;

use Getopt::Long;

my $sect_name  = "";     # Name of section
my $sect_unit  = "";     # Units defaults to inches
my $sect_depth = 0;      # Distance from origin
my $sect_plane = "";     # Plane, defaults to X-Y plane
my $sect_num   = 0;      # Number of points 

my $file_name;
my $fh;
my $help       = 0;
my $_debug     = 0;
my $val1       = 0;
my $val2       = 0;

my %vector_hdr;         # Headr information hash list
my @vector_pts = ();    # Array of x,y coordinates
my $vector_str = "";    #

my $top    = 'xy';
my $bottom = 'yx';
my $right  = 'zy';
my $left   = 'yz';
my $front  = 'zx';
my $back   = 'xz';


GetOptions(
        'file_name=s'  => \$file_name,
        'sect_name'    => \$sect_name,
        'sect_unit'    => \$sect_unit,
        'sect_depth'   => \$sect_depth,
        'sect_plane'   => \$sect_plane,
        'sect_num'     => \$sect_num,
        'help'         => \$help,
        'debug'        => \$_debug,
        );


if(!$file_name){
    print "No file was specified $!\n";
    help();
    exit;
}

#open file
open($fh, $file_name) or die "Failed to open file $file_name: $!";

#process file content
my $line_in;
my $key;
my $value;
my $seq_num = 0;
my $max     = 0;
my $plane;
my $coord_x;
my $coord_y;
my $coord_z;



while($line_in = <$fh>){
    chomp $line_in;
    if($_debug){print "processing: $line_in\n";}

    if($line_in =~ m/^sect_/){
        ($key, $value) = split(' ', $line_in);
        $vector_hdr{ $key } = $value;
    }
    else {
        # Put coordinates into 3D array
        # need test to skip lines with no data
            ($val1, $val2) = split(' ', $line_in);

            if($vector_hdr{'sect_plane'} =~ m/xy/){
                $vector_pts[$seq_num][1] = $val1;
                $vector_pts[$seq_num][2] = $val2;
                $vector_pts[$seq_num][3] = $vector_hdr{'sect_depth'};
            }

            # plot on front plane
            if($vector_hdr{'sect_plane'} =~ m/zx/){
                $vector_pts[$seq_num][1] = $val2;
                $vector_pts[$seq_num][2] = $vector_hdr{'sect_depth'};
                $vector_pts[$seq_num][3] = $val1;
            }

            # Plot on side plane
            if($vector_hdr{'sect_plane'} =~ m/zy/){
                $vector_pts[$seq_num][1] = $vector_hdr{'sect_depth'};
                $vector_pts[$seq_num][2] = $val2;
                $vector_pts[$seq_num][3] = $val1;
            }
            $seq_num = $seq_num + 1;
    }
}

exit;
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