Hi Charles,
As for a fiction film, structure is the core matter of documentary making. With the documentary though, you have the choice of going first for the pictures, and later on start the structuring at the editing stage; or have an outline of structure and then go chasing your pictures according to that structure. Either way, the bottom line is that you must have a teaser exposing what the documentary is about, and a dramatized development of what you exposed in the teaser.
Give you advice: go out there, rent a documentary film you liked and watch it alone in your room with a critical eye. See how the whole thing will unfold and you definitely will spot that it's got structure. If you are undecided as to what doc film to rent, I recommand you "bowling for Colombine", by Mike Moore or "Farenheit 9/11 by the same director. The subject it covers may be controversial, but the technique and the procédé used is professional above the standards of the industry.
To recap: You must structure your documentary. Gather your pictures, and knowing what you have got, you will then start the structuring thing at your Final Cut pro console. Alternatively, through your preliminary research you may have gathered a lot of information about your suject that can help you structure your movie beforehand, in which case shooting comes later. But such an a priori structure should remain flexible as everything is not bound to work out as you planned it on paper.
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