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

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After rooting using Nooter, your SD card is left with a partition that may be less than that of the SD card you're using. You'll want to fix this so that you can use the full capacity of your SD card again. Your Nook Device can fix this for you.

  1. Power up your Nook Device without the SD card inserted. (Otherwise it will try to boot off of the SD card.)
  2. Insert SD card.
  3. Pull up settings:
    • For Nook Color: Click the white arrow and then click the "Settings" button.
    • For Nook Touch: Click the "n" button and then click the "Settings" button.
  4. Then go to "Device Info"
  5. Then click on "SD card"
  6. Click on "Unmount SD card"
  7. Then click "Format SD card"

Your Nook Device will repartition and format the card to its full capacity.

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

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