Get a physical copy of your book. You need this so that it can be on file at the US Copyright Office.
Obtain US Copyright form SL-35. You can get this form on the US Copyright Office website (see Resources).
Decide on how you will register the book. When you get form SL-35 you have two options to copyright a book with a pen name. If you elect to list your real name on the form, as well as your pen name, the book will be given the standard copyright protection of life of the author plus 75 years. However, if you elect to only put the pen name on the form, then the book will only be protected for 95 years from the publication date or 120 years from the creation date, whichever is shorter. To register the pen name, be sure to check the box by "Pseudonymous" on the form.
Submit form SL-35. Once you complete form SL-35 you will need to submit it to the US Copyright Office with the filing fee. 2009 price: $45 by mail or $35 online. You can submit your form online on the website or you can mail it in to the address on the form.
Mail in your book. To complete the copyright process for your book with a pen name, you will need to mail in a copy of the actual book or manuscript to the address that is listed on form SL-35. You will not get this item back, as it will stay on file with the US Copyright Office.