"What did you write the letter with?"
Translation:Čím jsi napsal ten dopis?
It stresses napsal, but not too strongly. For example when you are surprised he was able to write it, you thought he had no pen or something. It can be used in the same situation as the official translation which stresses "dopis" more and can be also used to distinguish the letter from other things he may have written by other means. I will add it.