[{a1:"value a1",a2:"value a2"},{a1:"value a3",a2:"value a4"},{a1:"value a5",a2:"value a6"},{a1:"",a2:""}]

db.collection.aggregate([{$group:{_id:null,a1:{$push:"$a1"},a2:{$push:"$a2"}}},{$project:{a1:{$filter:{input:"$a1",cond:{$ne:["$$this",""]}}},a2:{$filter:{input:"$a2",cond:{$ne:["$$this",""]}}}}}])