The answer essentially lies in the wonders of the geology of the earth. The compression of the bones of dead dinosaurs that fell into bogs, rivers etc were compressed in mud which slowly turns to rock (I think!) this creates what we know as fossils, so we have the bone structures of each dinosaur.
After that, it is like a giant jigsaw puzzle to put the bones together in the right order to make a whole animal. Then it is a lot of academic guesses as to what they really look like – really we have no idea at all what colour they are, what the skin looks like, if they have feathers etc. As far as I know they are guesses, I would like a Paleontologist to tell me exactly how it works!
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