Database

[{"maxUserLevel":1,"subsystems":[{"sections":[],"name":"apple"},{"sections":[{"name":"banana"}],"name":"sun",},{"sections":[],"name":"orange"}],"systemID":"12345"},{"maxUserLevel":3,"subsystems":[{"sections":[],"name":"blue"},{"sections":[{"name":"pink"}],"name":"red",},],"systemID":"15654"}]

Query

db.collection.aggregate([{"$project":{"_id":1,"maxUserLevel":1,"subsystems":{"$filter":{"input":"$subsystems","as":"s","cond":{"$ne":["$$s.sections",[]]}}}}}])

Result