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

db.collection.aggregate([{"$addFields":{"array1":{"$map":{"input":"$array1","as":"a1","in":{id:"$$a1.id",array2:{"$map":{"input":"$$a1.array2","as":"a2","in":{id:"$$a2.id",array3:{"$filter":{"input":"$$a2.array3","as":"a3","cond":{$eq:["$$a3.status","done"]}}}}}}}}}}},{$match:{"array1.array2.array3":{$ne:[]}}}])