-e will test true if the file exists, and it'll also return false if the target exists, but isnt a file (directory). The same holds true for -d with respect to directories. Using these, your code would be written as follows:

@files = $ftp->ls;

foreach $file1 (@files) { 
  next if(-e $file1); # skip non-directories

  if(-d $file1) { 
    $ftp->get($file1) 
     || die "Can't get files from $dir :@{[ $ftp->message ]}\n";    
  }
}
$ftp->close();
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