Database
[{_id:"Id",username:"name",cars:[{_id:"BMW Car Id",name:"BMW",colors:[{_id:"color_red_id",color:"red"},{_id:"color_blue_id",color:"blue"}]},{_id:"Mercedes Car Id",name:"Mercedes",colors:[{_id:"color_yellow_id",color:"yellow"},{_id:"color_violet_id",color:"violet"}]}]}]
Query
db.collection.aggregate([{$project:{cars:{$filter:{input:"$cars",as:"item",cond:{$eq:["$$item.name","BMW"]}}}}},{$unwind:"$cars"},{$project:{cars:{$filter:{input:"$cars.colors",as:"item",cond:{$eq:["$$item._id","color_red_id"]}}}}},{$unwind:"$cars"},{$replaceRoot:{newRoot:"$cars"}}])