[{"id":"1","children":[{"id":"1","grandChildren":[{"id":"1","toys":[{"id":"1"}]}]},{"id":"2","grandChildren":[{"id":"1","toys":[{"id":"1"}]}]}]}]

db.collection.update({"id":"1"},{"$pull":{"children.$[child].grandChildren.$[grandChild].toys":{"id":"1"}}},{arrayFilters:[{"child.id":"1"},{"grandChild.id":"1"}]})