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I have 2 tiffs to mosaic which overlap and there is a order to display them right, When using Mosaic to New Raster the first file I input will be overlapped by the second input file?

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Reset to default
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There is a switch 'Mosaic Operator' which controls the order of layers. If you keep default which is 'LAST', the former will be overwritten by the latter as you assume.

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