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Minecraft uses a tree-structured file format known as "NBT" (kind of like JSON or XML, but not text-based). There are no fixed offsets which you can rely on. You will need to use a library to parse NBT (or write your own parser) and then extract the information you want from the parsed structure.
Easiest way for you to achieve that would be to use already created world engine. McEdit allows you to write plugins in python. You could write two plugins: First would load a file with points, create schematics of those regions. Second would load file with points and folder with schematics and paste them in. I don't know if McEdit can be used in a scheme: ...
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