You'll need to use the Connect software. While the Reader is connected, you just select the Sony Reader on the left hand side tree, and the book you want to delete on the RHS tree. Then hit the delete key and you should be done after maybe a confirmation dialog box.
If you put books on an SD card, you can manage the contents directly with an SD card reader also, but remember that the indexing is slow on the Reader, but almost instant with the desktop software.
I created a collection "Included Books" in my library before doing any deleting, and copied the Reader default contents into that collection first.
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