Database
[{"attr":"value","aray1":[{"pickme1":true,"data1":"jklsdjk","aray2":[{"pickme2":true,"data2":"treasure1"},{"pickme2":false,"data2":"trash1"},]},{"pickme1":false,"data1":"jklsdjk","aray2":[{"pickme2":true,"data2":"treasure2"},{"pickme2":false,"data2":"trash2"},]},]}]
Query
db.collection.aggregate([{$addFields:{aray1:{$filter:{input:{$map:{input:"$aray1",as:"a1",in:{aray2:{$filter:{input:"$$a1.aray2",as:"ia2",cond:{$eq:["$$ia2.pickme2",true]}}},pickme1:"$$a1.pickme1",data1:"$$a1.data1"}}},as:"oa1",cond:{$eq:["$$oa1.pickme1",true]}}}}},{"$project":{result:"$aray1.aray2",attr:1}},{"$project":{"result.data2":1,attr:1}}])