Thank you Mary and Ken for your replies.
Maybe I do not do it in the right way. Let's say I have a course with x topics, say 20. I want to create a new course with 5 of these topics. So I backup the 5 topics and restore them in a new course. The new course includes the 5 topics but also 15 empty topics.
Not a big problem, just a little annoying because I have to delete the empty topics.
As Mary wrote, when Moodle restores some activities, it restores them in the same section number they where in the course when the backup was done.
That generates empty sections for you, but at the opposite, if you want to add things to an existing course with all sections already filled, it creates doubles in the sections. See MDL-61100 about that. It could also be made to answer your problem, if sections are created just when no sections are used in the destination course.
What you could try (not sure of the result) is to move the sections you want to copy in the first sections of your original course before doing the backup, and then try to restore to a new course.