Two other ideas:
1) I haven't tried it, but while reviewing the man page for wget, I noticed the option --delete-after. Perhaps it would leave the directory structure behind after getting and deleting the local files.
2) A while ago, i wrote a program using Net::FTP to get hierarchical collections of files. I just chopped it up to give you a starting point:

#!/usr/bin/perl -w
#==============================================================
# GetDirHierarcy.pl
#==============================================================
use strict;
use warnings;
use Net::FTP;

my $host = 'your.ftp.server';
my $uid = 'user_id';
my $pwd = 'pa$$word';

my $ftph = Net::FTP->new($host) or die "Can't connect to $host";
$ftph->login($uid,$pwd) or die "Can't login";


&GetFiles(".");
$ftph->quit;

sub GetFiles {
    my $pref = shift;
    # NOTE: Assumes UNIX ls format!
    #my @DirList = grep {/^d/} $ftph->ls;
    my @DirList = $ftph->dir;
    for my $DirEnt (@DirList) {
        next if $DirEnt !~ /^d/;
        my $DirName = (split / +/, $DirEnt, 9)[8];
        my $newpref = $pref . '/' . $DirName;
        print "mkdir $newpref;\n";
        $ftph->cwd($DirName);
        GetFiles($newpref);
        $ftph->cwd("..");
    }
}
[download]

Running this against an FTP server I have access to gives:

$ ./GetDirStruct.pl
mkdir ./Files;
mkdir ./Files/Bar;
mkdir ./Files/Bar/Baz;
mkdir ./Files/Foo;
mkdir ./Inquiry;
mkdir ./NpcIN;
mkdir ./Processing;
mkdir ./Security;
mkdir ./Sysmenu;
[download]

Just edit the print statement to actually make it create the directory hierarchy.
NOTE: You may encounter an oddball FTP server that uses a different format for the DIR command. (I don't think that the results of the DIR command are in the FTP standard.) So you may have to edit the directory-name parsing portion of the code for your server. (I ran into this problem on an IBM mainframe FTP server.)
--roboticus