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It would be much more satifying to have just a generic pile of protons, electrons, and nuetrons at one end (with perhaps some amount of their antimatter equivalents if needed), and the process arranges them into the atoms from the original material you want duplicated. Instead of having like kind atoms at one end just being remade into a different pattern of the same atoms, because then you would have to know what is being "sent" before hand and have the exact materials on hand. The generic method means you don't need specific atoms, just building blocks for any atomic pattern.
At least that would be ideal from a fuctional use. Practical use and energy viability is where things "fall apart" in sci-fi to reality development.
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