Well, does a MongoDB ReplicaSet/Cluster duplication for backup or test purposes sound like an obvious task?
Think again :-)
There is no magic button or anything like that, but there are a few tools that can be used to complete this task:
Backup and Restore
Use mongodump and mongorestore to backup your current instance and restore to a new instance. To save bandwidth and minimize time, make sure you use an instance in the cloud vendor region matching your MongoDB ATLAS.
Use the mongomirror to migrate the data to the new cluster. Please notice the mongomirror do not copy config and permissions.
I believe the backup/restore method might be best in most cases, but you can have it your way