See Rooting new hardware FIRST if you have a nook original with a 1003* serial# or above.

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NookColor Format and partition your SD card back to a usable state

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Part of the NookColor portal

After rooting using nooter, your SD card is left with a single 40mb partition on it. You'll want to fix this so that you can use the full capacity of your SD card again. The Nook Color can do this for you.

Power up your Nook Color *WITHOUT* the SD card inserted (Otherwise it will try to boot off of the SD card)
Tap the white arrow on the status bar to pull up the context menu with device "settings"
Then go to 'Device Info'
Then click on 'SD card'
Click on 'umount sdcard'
Then click 'format sdcard'

The NC will repartition and format the card to it's full capacity.

Source: http://forum.xda-developers.com/showpost.php?p=9677291&postcount=2

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