Thank you for the reply. When I put the print command at the end of the file, all the duplicates are still there. My original code had this snippet at the end:

open(my $fh1, '>', $SCAC_output) ;
foreach (@output) {
    print $fh1 "$_ \n ";
}
close $fh1 ;
[download]

The $SCAC_output file (defined elsewhere in the code) has a bunch of duplicate file references from the array. The reason I ended up putting the print statement inside the while loop (along with the sleep command) was to try to understand better what part of the code causes duplicates in the array.

When i run this

#!/usr/bin/perl
use strict;
use warnings;
#use WWW::Mechanize ;
#my $mech = WWW::Mechanize->new();

my $txt_url ;
my $pdf_url ;
my $html_url ;
my $output ;
my @output ;
#my $file_content = "D:/Perl/Perl output/garbage_content.csv" ;
my $file_content = "1189436input.txt" ;

#    my $get_file = "http://securities.stanford.edu/filings-case.html?
+id=101092";
    my $filename = "file_output_101092" ;
#        my $response = $mech->get($get_file,
#        ':content_file'=> $file_content,);
    open my $fh, '<', $file_content  or die $?;

      my $i =1 ;
         
      while (<$fh>) {
      chomp;

$txt_url=''; 
$pdf_url=''; 
$html_url=''; 

       if(index($_,".txt")>=0) {
         $txt_url = $_ ;
        }else {
      if(index($_,".pdf")>=0) {
          $pdf_url = $_ ;   
        }else {
      if(index($_,".html")>=0) {
          $html_url = $_ ;   
      } 
    }
  }
 
        if (($txt_url)|($pdf_url)|($html_url))
        {
            $output = join ",", $filename, $txt_url, $pdf_url, $html_u
+rl ;
            push @output, ($output) ;
   }
}

close $fh ;

            foreach (@output) {
                print "$_\n" ;
            }
[download]

i get this

file_output_101092,,,                <a href="index.html">Home</a>
file_output_101092,,,                <a href="filings.html">Filings Da
+tabase</a>
file_output_101092,,,                <a href="resources.html">Resource
+s</a>
file_output_101092,,,                <a href="litigation-activity-indi
+ces.html">Litigation Activity Indices</a>
file_output_101092,,,                <a href="clearinghouse-research.h
+tml">Clearinghouse  Research</a>
file_output_101092,,,                <a href="about-the-scac.html">Abo
+ut</a>
file_output_101092,,,              <!-- <div style="float: left;positi
+on: relative;top: 5px;"><a href="filings.html">Browse Filings Databas
+e</a></div> -->
file_output_101092,,,              <!-- <div style="float: left;positi
+on: relative;top: 5px;"><a href="filings.html">Browse Filings Databas
+e</a></div> -->
file_output_101092,,,                                                 
+                                                            <tr class
+="table-link" onclick="window.location='filings-documents/1010/ALTSE9
+8/001.html'" target="_blank">
file_output_101092,                                                   
+    <tr class="table-link" onclick="window.location='filings-document
+s/1010/ALTSE98/000.txt'" target="_blank">,,
file_output_101092,,                                                  
+                                                            <tr class
+="table-link" onclick="window.location='filings-documents/1010/ALTSE9
+8/19981029_r04c_9800528.pdf'" target="_blank">,
file_output_101092,,                                                  
+    <tr class="table-link" onclick="window.location='filings-document
+s/1010/ALTSE98/1999730_r07o_98CV00528.pdf'" target="_blank">,
file_output_101092,,                                                  
+    <tr class="table-link" onclick="window.location='filings-document
+s/1010/ALTSE98/1999830_r04c_98CV00528.pdf'" target="_blank">,
file_output_101092,,                                                  
+    <tr class="table-link" onclick="window.location='filings-document
+s/1010/ALTSE98/2002726_r03k_9800528.pdf'" target="_blank">,
file_output_101092,,,   <div class="span12"><p><a href="filings-case-p
+ages-url-map.html" style="color: #ffffff"><strong>Cases</strong></a><
+/p></div>
file_output_101092,,,                           <legend  style="margin
+-left: 0px;margin-bottom: 0px"><a href="about-the-scac.html" style="c
+olor: #565656">About</a></legend>
file_output_101092,,,                                           <dd><a
+ href="about-the-scac.html#about" style="color: #151616">About Us</a>
+</dd>
file_output_101092,,,                                           <dd><a
+ href="about-the-scac.html#methodology" style="color: #151616">Method
+ology</a></dd>
file_output_101092,,,                                           <dd><a
+ href="about-the-scac.html#faq" style="color: #151616">FAQ</a></dd>
file_output_101092,,,                                           <dd st
+yle="color: #565656"><a href="about-the-scac.html#sponsors" style="co
+lor: #151616">Sponsors &amp; Partners</a></dd>
file_output_101092,,,                                           <dd><a
+ href="about-the-scac.html#register" style="color: #151616">Register<
+/a></dd>
file_output_101092,,,                                           <dd><a
+ href="about-the-scac.html#contacts" style="color: #151616">Contact U
+s</a></dd>
file_output_101092,,,                                           <dd><a
+ href="about-the-scac.html#legal" style="color: #151616">Legal Notice
+s</a></dd>
file_output_101092,,,                                           <!-- <
+dd><a href="about-the-scac.html#sitemap" style="color: #151616">Site 
+Map</a></dd> -->
[download]

I assume that the few "duplicates" there are from multiple references in the page or "#" references

Yes, I see that the problem was that the $txt_url, $html_url, and $pdf_url variables were never reset to null when the new input did not have a txt, html, or pdf reference. Thus, those variables were re-inserted into the array every time a new line was read in. Your code solves the problem. I appreciate the help!