Mongo cluster - simple backup question
You could use:


backup software (for automated snapshots of your data),
mongodump/mongorestore,
or a simple copy of the \data\db directory to your backup location.


For option 2, make sure to use mongodump with the --oplog option. If you need to restore, then use mongorestore with the --oplogReplay option.

With option 3, stop the secondary member, and copy the the data out. Or, if you do not desire to stop the secondary, use db.fsyncLock(), backup and then use db.fsyncUnlock().

Secondaries replica set members are ideal for reporting and backup use cases. 

Reference: https://docs.mongodb.com/v3.2/core/backups/