That smell is the smell of the protein in your nails breaking down. It should be similar to the smell of your hair burning. In addition, because the composition of the protein is different for every person, everybody's nails will smell different. Mine, for example, smell something like buttered popcorn.
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Nails can stink for two reasons after being filed. The strong smell from the emery board used to file the nail can cause it to stink. The protein in the nail will also cause an odor when filed down.