[{"_id":{"$oid":"61b253a89e51973f978b818d"},"id":1,"level1":[{"name":"child11","level2":[{"name":"chil21"},{"name":"chilxx"}]},{"name":"child12","level2":[{"name":"chil23"},{"name":"chil24"}]}]},{"_id":{"$oid":"61b254b69e51973f978b818e"},"id":2,"level1":[{"name":"child13","level2":[{"name":"chil25"},{"name":"chil26"}]},{"name":"child14","level2":[{"name":"chil27"},{"name":"chil28"},{"name":"chilxx"},{"name":"chil2a"}]}]}]

db.collection.aggregate([{"$match":{"level1.level2.name":"chilxx"}},{"$set":{"level1":{"$filter":{"input":"$level1","as":"first","cond":{$ne:[{"$filter":{"input":"$$first.level2","as":"second","cond":{$eq:["$$second.name","chilxx"]}}},[]]}}}}}])