A student wrote with the question above. Find my response below:
Structure refers to methods of the organization of ideas or content, as in comparison and contrast, chronological, least important to most, etc. Format deals more with how a document is laid out in terms of appearance. There is some overlap between the two, and no doubt this overlap and how loosely I've used the terms is the source of some of your confusion.
Let me know if you need any further clarification.