NatNet does not contain any functionality for recording or exporting data. You would need to add that to your NatNet client if that is what you are hoping to do.
Otherwise CSV's can be manually exported from Motive itself if you have recorded the data there.
we are struggling in manipulating the data received from Motive,
Is there a way to automate csv export not necessarily using NatNetClient?
maybe through setting changes in Motive?
You could try using the Batch Processor and Python or C# to automate CSV export. This would require that you at least launch the application and add the takes that you want to export though.