Another tool that can do this: mtree
It first appeared on bsd systems, there are ports for linux too. In Ubuntu it is in package 'mtree-netbsd' or 'freebsd-utils'.
# 1: cd to your source dir
cd my_source_dir
# 2: create a specfile. Place the spec outside of the sourcedir and destdir
mtree -c > /tmp/myspec.txt
# 3: cd to the destdir
cd my_dest_dir
# 4: now create only the dir structure from the specfile
# -u is for creating only dirs, it does not follow links
mtree -f /tmp/myspec.txt -u
If you later deleted some dirs in the destdir call the command form step 4 again, dir-structure will be restored.
mtree can do a lot more. follow links, create/delete specific files/dirs, delete or not delete files that are in the destdir...