Why won't something like this work? What problems were you having with CGI?

<form enctype='multipart/form-data' ...>
<input type='file' name='file' ...>
<input type='file' name='file' ...>  (repeat)

use CGI ':standard';
use File::Basename;

foreach (param('file')) {
   my $basename = basename($_);
   $basename =~ tr/A-Za-z0-9.//cd;    # strip out unwanted crap
   open(FILE, "> $basename") or die "$basename: $!";
   print FILE <$_>;
   close(FILE);
}
[download]

You may have to tweak fileparse_set_fstype to match the OS of the client (see File::Basename and CGI, perhaps using $ENV{HTTP_USER_AGENT}). I haven't tested this, but is something like this what you were wanting to do?