Phew, your indentation is overwhelming! Consider these examples to help:

   #move this line up (and simplify it):
   #if(length($materialmapping_file) gt 0 or length($data_folder) gt 0
+)
   unless (defined $materialmapping_file and defined $data_folder)
   {
      print "Usage: $0 <materialmapping_file> <data_folder>\n";
      exit;
   }

   # Now, everything that follows can be outdented one level.
[download]

Similarly:

   while( ($filename = readdir(DIR))){
      #if($filename =~ /\.xls$/i) {
      next unless $filename =~ /\.xls$/i;
      # everything below can be outdented    
    
      my $parser     = Spreadsheet::ParseExcel->new();
      my $oBook  = $parser->parse($data_folder.$filename);
      #if (defined $oBook ) {
      next unless defined $oBook;
      # everything below can be outdented
      ...
[download]

For your duplication problem, I think this might do:

my %seen;  # a new global variable
...
   # then, whenever you 'createElement' and/or 'setAttribute', first a
+ssemble the string:
   #my $materialmapping_item2 = $materialmapping_table_xml->createElem
+ent("item3");
   #$materialmapping_item2->setAttribute(decode('cp1252',$pr_cell_name
+2->{Val}),$pr2);
   my $entry = join',', decode('cp1252',$pr_cell_name2->{Val}),$pr2;

   # and create it if it doesn't already exist:
   if (!exists $seen{$entry}++){
      my $materialmapping_item2 = $materialmapping_table_xml->createEl
+ement("item3");
      $materialmapping_item2->setAttribute($entry);
   }
[download]