I am using ArcGIS Desktop 10.0.
I have a trick for removing the donut holes, which is converting the polygon to line and then creating polygon out of the lines and in the end merging all of them. The drawback of this strategy is that in removes other holes and empty areas which in reality are empty and should be kept empty. See below image:
Answer
I would try the Union tool with NO_GAPS:
NO_GAPS —A feature will be created for the areas in the output that are completely enclosed by polygons. This feature will have blank attributes.
You can then select the features with blank attributes below a threshold size and calculate their attributes to be the same as the original polygon - or copy/paste them in the Editor's Attribute window.
Features with blank attributes above the threshold size should be deleted.
From there the Dissolve tool should complete the job.
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