$newFile = `grep -l $commonField $responseDir/*`;
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Read in perlop about `` (aka qx). If you want just one result, use qx in list context: ($newFile) = `...` but be aware that it will have a newline appended, so chomp($newFile) afterwards. I don't have the sense that you are trying pieces of your solution individually; I think you will find this much easier than repeatedly trying small changes in your whole script. I get undef from from `grep -l nosuchmatch *`, for instance.

I had to do a very UGLY hack to make it work, Any suggestions on imporvment will be great

foreach $arrFileList(@arrFileList)
 {
   print "I am doing this file $arrFileList\n";
   open (FILE, "$sourceDir/$arrFileList") or die "could not open $sour
+ceDir/$arrFileList: $!\n";
   @Lines = <FILE>;
   close FILE;
   $origField = (split /\|/, $Lines[3])[-3];
   $commonField = (split /\|/, $Lines[13])[-1];
   $commonField = "NX2\\|01\\|" . $commonField;
   chomp $commonField;
   print "my commonField is this $commonField\n";

   $newFile = `grep -l $commonField $responseDir/*`;
   chomp $newFile;
   print "my newFile to change is $newFile\n";

   if ($newFile =~ "/")
    {
      system ("perl -pi -e 's/$replaceField/$origField/g' $newFile");
      print "Done doing perl s/$replaceField/$origField/g $newFile\n";
      system ("mv $newFile $responseDone");
      print "Done moving $newFile to $responseDone\n";
      system ("mv $sourceDir/$arrFileList $processed");
      print "Done moving $sourceDir/$arrFileList to $processed\n";
    }
 }
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