Here are some examples of things that would be considered "Structure" for the whole program:
The directory layout of your code.
All of the classes and how they relate to each other.
The structure (schema) of the database, if your program uses a database.
Note here that the actual data in the database isn't part of the Structure, though. If your program is producing the data and then sticking it into the database, then that's part of the Result. If the data is sitting in the database and your program is supposed to process it, then that data is part of the Input.
Then an individual class (and I mean a "class" in the object-oriented sense) would also have a Structure:
The names of methods in the class and the types/names of parameters that they take.
The names and types of variables (member variables) in the class.
Whether or not a function (or variable) is private or public would also be part of the Structure, because Structure describes what something is (as opposed to what it does or...