The Fantastic Four defeat Dr. Doom (Julian McMahon) by heating up his metal body and then supercooling it, causing it to solidify. The frozen Doom is then placed in a crate on a ship bound for his home country of Latveria, but as the film closes, we see a slight manifestation of his powers (Duh-duh-DUH!)
Thanks, Herbmeistr and Petri Dish Kid!
(Links open in new window)
Read more about this film at The Internet Movie Database.