masking or clipping rasters

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I created a water district boundary polygon that I have used to clip several raster data sets. However, my polygon contains areas marked as 'exclusions' which are spots within the overall boundary that are actually not included in the water district. Is there a way to 'punch out' these exclusion areas from the raster? Either mask them so they aren't included in any area calculations or further analysis, or somehow cut them out entirely?



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