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If you are talking about radical changes to the height shape and form of the character then you are referring to changes in the mesh and skeleton of the model.
Think of it this way :a 3d game model is made up of a series of connected "bones" that have a series of preset animations. This skeleton is covered with a "mesh" made up of polygons or triangles.That mesh is then mapped or covered in a skin. You can make changes to the skin, usually in a program like photoshop,but that will only alter the appearance of it.
If you want to alter the size and shape or change the anatomy of a model, then you have to use a program like 3D studio Max or Milkshape 3D. You then extract the player model from the games developement kit (if there's one included).There usually is a restriction to the polycount of the model for the particular games engine. If you add too much detail, the game can't run it. If you alter the over all shape of the model, then you would have to re-animate the skeleton.This can be a very complicated process, but there are tons of tutorial sites for beginners.
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