They (/we, I'm just testing armour modeling now) use a body model, otherwise we wouldn't know any measurements/body proportions, or at least that's how I think everyone is doing, don't know how the heck you would make them otherwise
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But all armours are made from scratch if that is what you meant, of course, if you have made an armor you could technically use it to help you make a new armour, but it's often easier to remake from scratch.
Any program is good, use the one you are most used to, I use 3ds max, some use blender i guess (I dont like blender >_>) etc etc.
//edit
I downloaded the environment armour and I'm not sure how the skin works :S A part of the armor was modeled (like normal) but a large part of the "armour" was just a texture on the skin. Was it an in-complete version or what :/