Download the file to your desktop or anywhere convenient.
It's in the Garmin/Waypoints directory in the NUVI and is called
It's probably a good idea to back this file up anyway from time to time, in case something happens.
You can also format it from the SD card reader in Ubuntu, but I don't know the exact commands.
I have a Canon camera that formats it in a few seconds, so I don't need to.
(This does not use wine, Ubuntu can read and write to the NUVI natively without problems).