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Assuming both datasets are accurate you can subtract or add one from the other. In Esri use Raster Calculator (spatial analyst extension required); You can also use GDAL_Calc on command line or QGIS raster calculator. If your flood data is just the depth of flooding then you can add the two to get the flood level, if it's the bottom of the channel you want ...


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The question (as clarified in a comment) asks how to remove local slope to calculate relative ruggedness. There is a simple way to do this. It relies on computing the slope using the same local data as the ruggedness (which usually is a 3 by 3 square neighborhood). I recall verifying that ArcGIS computes slope (s) and aspect in exactly this manner: ...



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