I propose a division of the literature on natural kinds into metaphysical worries, semantic worries, and methodological worries. I argue that the latter set of worries, which concern how classification influences scientific practices, should occupy centre stage in philosophy of science discussions about natural kinds. I apply this methodological framework to the problems of classifying chemical species and nanomaterials. I show that classification in nanoscience differs from classification in chemistry because the latter relies heavily on compositional identity, whereas the former must consider additional properties, namely, size, shape, and surface chemistry. I use this difference to argue for a scale-dependent theory of scientific classification.