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Otoliths are small structures in fish ears made of calcium carbonate which carry a record of the environment in which the fish live. Traditionally, in order to study their microchemistry by a scanning technique such as PIXE the otoliths have been either ground down by hand or thin sectioned to expose the otolith core. However this technique is subject to human error in judging the core position. In this study we have scanned successive layers of otoliths 50 and 100 µm apart by removing the otolith material in a lapping machine which can be set to a few µm precision. In one study by comparing data from otoliths from the two ears of a freshwater species we found that polishing by hand could miss the core and thus give misleading results as to the life cycle of the fish. In another example we showed detail in a marine species which could be used to build a three dimensional picture of the Sr distribution.