Introduction - 2 ways of doing this
There are 2 ways to create the form of the paper model (just the blank model, without the graphics).
1: Using computer software
The first way is to use simple 3D modelling software combined with this application called Pepakura Designer which automatically unfolds 3D data into 2D form on paper. This way is commonly used to build paper toys that are made up of many complex polygons, such as video gaming characters.
Link from Legend of Zelda, by Ninjatoes
What you see above is an example of a paper model that is impossible to design by hand. The reason is, the character is made of many complex polygons, which are near impossible to measure, account for the many complex angles and conceptualise all in your head!
What Ninjatoes did was to acquire 3D data of Link from the game - this can be done either with 3D data capture software, or simply request the creators of the game to supply you with the required files. Later he used Pepakura Designer to unfold the 3D data into a 2D paper template.
2: Pencil and paper
The second way is to go back to basics using pencil and paper to design the parts, testing them to see if they fit as you go along.
I personally favour this method, because it's much more versatile in certain aspects. Also, if you really just need a simple part to be modelled, it's alot easier to just draw it out, than to go through all the steps required in the first method.
However, if your model requires complex polygonal shapes, you most definitely have to use the first method!
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