Once again I appreciate your guys' help a lot I'm still fairly new to PERL ok here is the code with the changes made and also another bit of code I have Added

#!/usr/bin/perl 
use warnings;
use strict;

 my $inFile = "UnSortReport.txt";
 my $outFile = "SortedReport.txt";
    open IN, "< $inFile";
    open OUT, ">> $outFile";
    
    my @not_sorted = <IN>;
    print OUT "|CSED Form|OrderNumber|Date|Total Documents|Total Pages
+|\n";
        @sorted = sort { lc($a) cmp lc($b) } @not_sorted; # alphabetic
+al sort
        my $count = 0;
        foreach(@sorted)
            {
            $frmType = substr $_, 1, 4;
            if ($frmType eq "M729")
                {
                print OUT "$_";
                $count ++;
                }
            else 
                {
                print OUT "There were $count Monthly 729 runs\n";
                }
            }
$count = 0;
        foreach(@sorted)
            {
            $frmType = substr $_, 1, 4;
            
            if ($frmType eq "M737")
                {
                print OUT "$_";
                $count ++;
                    }
            else 
                {
                print OUT "There were $count Monthly 737 runs\n";
            
                }
            }
$count = 0;
            foreach(@sorted)
            {
            $frmType = substr $_, 1, 4;
            
            if ($frmType eq "Q569")
                {
                print OUT "$_";
                $count ++;
                }
            else 
                {
                print OUT "There were $count Quarterly 569 runs\n";
                }
            }        
 close OUT;
 close IN;
 ##############The code Bellow looks a the SortedReport.txt and checks
+ for duplicate lines and removes them if any#########################
+###
    my $file = 'SortedReport.txt';
    my %seen = ();
    {
    local @ARGV = ($file);
    local $^I = '.bac';
        while(<>)
        {
        $seen{$_}++;
        next if $seen{$_} > 1;
        print;
        }
    }
print "finished processing file.\n";
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