[{"level1":[{"id":1,"level2":[[{"id":1},{"id":2},{"id":5}],[{"id":3},{"id":4}]]}]},{"level1":[{"id":1,"level2":[[{"id":1},{"id":2},{"id":5}],[{"id":7},{"id":4}]]}]}]

db.collection.find({"level1.level2":{$elemMatch:{$elemMatch:{id:3}}}})