[{"name":"somename","level":"123","nested":[{"somefield":"test","file":{level:"123"}},{"somefield":"test2","file":{level:"124"}}]}]

db.collection.aggregate([{$match:{$expr:{$in:["$level","$nested.file.level"]}}},{$project:{nested:{$filter:{input:"$nested",cond:{$eq:["$$this.file.level","$level"]}}}}}])