import arcpy
import os
arcpy.env.overwriteOutput = True

def iter_geom(g):
    for i in xrange(g.partCount):
        yield i, g.getPart(i)

def fill_donut_holes(polys, output, fill_threshold=0):

    # fields
    fields = [f.name for f in arcpy.ListFields(polys)
              if f.type not in ('OID', 'Geometry')
              and 'shape' not in f.name.lower()]

    # loop thru geometry
    geom = {}
    with arcpy.da.SearchCursor(polys, ['SHAPE@'] + fields) as rows:
        if fill_threshold:
            for row in rows:
                print row[0].partCount
                if row[0].partCount > 1:
                    array = arcpy.Array()
                    for i, p in iter_geom(row[0]):
                        pg = arcpy.Polygon(p).area
                        print pg
                        if pg >= fill_threshold:
                            array.add(p)
                    geom[arcpy.Polygon(array)] = row[1:]
                else:
                    geom[row[0]] = row[1:]
        else:
            for row in rows:
                array = arcpy.Array()
                for i, part in iter_geom(row[0]):
                    for pt in iter(lambda: part.next(), None):
                        array.add(pt)
                geom[arcpy.Polygon(array)] = row[1:]

    # create output
    path, name = os.path.split(output)
    sm = 'SAME_AS_TEMPLATE'
    arcpy.CreateFeatureclass_management(path, name, 'POLYGON', polys,
                                        sm, sm, polys)

    # insert rows
    with arcpy.da.InsertCursor(output, ['SHAPE@'] + fields) as irows:
        for geometry, attributes in geom.iteritems():
            irows.insertRow((geometry,) + attributes)

    arcpy.AddMessage('Created "{0}"'.format(output))
    return output