Here is the Working code

package LSRfm::Application::Upload;

use strict;
use warnings;
use base qw(LSRfm::Base);

use Apache::Reload;
use CGI;
use CGI::Upload;
#use CGI::Simple;

sub setup {
  my $self = shift;
  $self->start_mode('input');
  $self->run_modes([qw/input process/]);}

sub input {
  my $self = shift;
  my $errs = shift;
  my $html_template = $self->param('html_template');

  my $output;

  $html_template->process('upload/form', {wrapper => $self->wrapper(),
                    errors => $errs}, \$output)
           || die $html_template->error;
  return $output;
}

sub process {
  my $self = shift;
  my $html_template = $self->param('html_template');
  my $q = $self->query;
  my $script = $q->script_name;

  my $filename = $q->param('uploaded_file');
  my $from;
  my $fh = $q->upload('uploaded_file');
  my $diff_name = $q->param('diff_name');
  my $totalbytes;
  my ($bytesread, $buffer);
  my $num_bytes = 1024;
  my $destination = "/home/lsrfm/webs/www.lsrfm.com/htdocs/uploads/";

#check rm
  my ($results, $err_page) = $self->check_rm('input',
                                   {
                                     required => [qw/uploaded_file/],
                                     filters => ['trim'],
                                     msgs => {
                                               missing    => 'Please S
+upply a File Name',
                                             }
                                   });

  return $err_page if $err_page;

#sall good patch together
#  if ($diff_name)
#  {
#  $filename = $diff_name;
#  }
  my $output_file = $destination . $fh;
#upload time

  open (OUTFILE, ">", "$output_file") or die "Couldn't open $output_fi
+le for writing: $!";

  while ($bytesread = read($filename, $buffer, $num_bytes)) {
    $totalbytes += $bytesread;
    print OUTFILE $buffer;
  }
  die "$output_file Read Failure: $!" unless defined($bytesread);
  unless (defined($totalbytes)) {
    print "<p>Error: Could not read file $filename, ";
    print "or was of zero length";
  } else {
    print "<p>Done ok, $totalbytes</p>";
  }
  close OUTFILE or die "Couln't Close file $!";

#output
  my $output;

  $html_template->process('upload/form', {wrapper => $self->wrapper(),
                    status => "sall_good",
                    file => $filename,
                    dest => $destination,
                    from => $from,
                    }, \$output)
           || die $html_template->error;
  return $output;

}

1;
[download]

Dont forget to set the enctype of your form to enctype of "multipart/form-data"