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When you hook your Kindle up via USB port, it is essentially another flash drive on your computer.  You can pretty much do anything on it you would any other storage device.

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From the Kindle User's Guide:
"More about "My Clippings"
Once a bookmark, note, highlight, or clipped page is added to the "My Clippings" file, it cannot be removed individually from the "My Clippings" file. You can edit the "My Clippings" file on your computer and save it back to your Kindle if you want to edit the
contents of the file. Alternatively, you can move or remove the "My Clippings" file from Kindle and a new one will be created the next time you add a clipping or annotation to any content. Altering your "My Clippings" file does not affect any notes, bookmarks, or highlights you've made in individual documents. Those items will still be present the next time you open an item for reading, and you will be able to use them for navigation and reference. Also, the "My Clippings" file is simply a storage place for the notes you make. While viewing the file, you cannot navigate through to the materials referenced in the file."
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