Note: your script shouldn't work as is, because $ftp->get needs a single file name as argument, while you're giving a wildcard. That means you need to find out the exact name of the file to transfer, before the transfer. One way to do so is:

my @files=$ftp->ls or $error=1;
$ftp->quit if $error;

foreach(@files)  
{
  if (/^yourRegex/i)   #Filter file names

  {
     print "$_\n";
     unshift @match, $_; 
  }
}
defined $match[0] ? $fname = $match[0] 
                  : $ftp->quit;
[download]

So you list the files, and grab the filenames... Then you download the files... Then you run MD5 on them.

On the server side, you can run MD5 on the files on a schedule, or "upon arrival"; then you transfer MD5 file as well and match it to your local result - voila!

Hope this helps...