I think you shoud check your array before printing entries 13 and 14, I suspect they're indeed un initialized.
Try doing:

#! /usr/local/bin/perl -w

use strict;

open (FILEHANDLE, $ARGV[0]) or die "unable to open file";
open (OUTFILE, ">$$.output");

my @array;

while (<FILEHANDLE>)
{
chomp;

@array = ();
@array = split(/\s+/);

if (defined($array[13]) && defined($array[14])) {
  print STDOUT "$array[13]\t$array[14]\n";
  print OUTFILE "$array[13]\t$array[14]\n";
}
[download]

Thanks.

Hotshot