[{"_id":1,"members":["a1","a2"],"member_profiles":[{"_id":"a1","is_removed":true}]},{"_id":2,"members":["a1","a3"],"member_profiles":[{"_id":"a3","is_removed":true}]}]

db.collection.aggregate([{$unwind:"$member_profiles"},{$match:{"member_profiles.is_removed":true}},{$group:{"_id":"$_id",members:{"$first":"$members"},member_profiles:{"$push":"$member_profiles"}}},{$project:{"activeMembers":{$filter:{input:{"$map":{"input":"$members","as":"m","in":{"$cond":{"if":{"$in":["$$m","$member_profiles._id"]},"then":null,"else":"$$m"}}}},as:"mem",cond:{$ne:["$$mem",null]}}}}}])