The following example demonstrates how to remove graphs which are related to empty graphs:

PREFIX nrl:<http://www.semanticdesktop.org/ontologies/2007/08/15/nrl#>
SELECT ( bif:exec(bif:sprintf("SPARQL CLEAR GRAPH<%s>", str(?mg))))
WHERE
  {
    ?mg nrl:coreGraphMetadataFor ?g .
    FILTER(?g in ( <urn:nepomuk:local:8a9e692a> )) .
    FILTER ( !bif:exists((SELECT (1) WHERE { GRAPH ?g { ?s ?p ?o . } . })) ) .
  }