[{"logfile1(unknown)":[1,2,3]},{"logFile2(unknown)":[4,5,6]}]

db.collection.aggregate([{$group:{_id:"$_id",new:{$first:"$$ROOT"}}},{"$project":{"map":{"$objectToArray":"$new"}}},{$match:{"map.v":1}},{"$project":{"map":{"$arrayToObject":"$map"}}},{$replaceRoot:{newRoot:"$map"}}])