db={"sample":[{"_id":"1234","array1":[{"id":"a11","array2":[{"id":"a21","array3":[{"id":"a31","status":"done"},{"id":"a32","status":"pending"}]}]}]},{"_id":"4321","array1":[{"id":"a11","array2":[{"id":"a21","array3":[{"id":"a31","status":"pending"},{"id":"a32","status":"pending"}]}]}]}]}

db.sample.aggregate([{$addFields:{newArray:"$array1"}},{$unwind:"$newArray"},{$unwind:"$newArray.array2"},{"$match":{"newArray.array2.array3.status":"done"}},{"$unset":"newArray"}])