This is a similar question to Deleting polygon defined area from raster layer in ArcGIS Desktop?, but I need the answer to be able to apply to multi bands since I am working with a RGB file. I have a Landsat 8 file and have used SAGA to classify the clouds (wasn't to fond with ArcMaps). I I want to use arcmap to remove the polygon clouds from my original landsat image (SAGA is too slow and crashes constantly). From the post linked above, I have converted the shape file to a raster.
I was thinking may changing all the cloud raster values to zero (not sure how to do this) and then multiplying with the original landsat 8 raster.