Choose a pseudonym you believe matches your writing style and genre. Keep in mind that once you are published, you will be referred to by that name and not your real name. Consider using a variation of your first name or nickname in order to avoid confusion when you are addressed in public.
Search online for your chosen pseudonym. Use search engines, libraries and book retailers. Don't be discouraged if another author has your pseudonym but publishes in a different genre -- for example, you write mysteries and the other author writes technical manuals.
If the author writes in the same genre or a similar genre such as suspense, consider changing your pseudonym.
Go to a domain name registration service website and enter your pseudonym. You will have the option to choose different extensions such as .com, .net, etc. Your pseudonym may already be claimed by one extension but available in another.
If your pseudonym is claimed in multiple extensions, consider using another pen name. If it is available in your chosen extension, purchase it.
Format your manuscript using both your real name and your pseudonym. On the first page, type your contact information in the upper left corner. Your pen name will go above your real name and be followed by "pseudonym" in parenthesis. For all subsequent pages, use the last name of your pseudonym in the header.
Follow the guidelines of the editor or agent you are submitting your manuscript to. Guidelines can be found on their website.
Use your real name for your query or cover letter and explain that you are writing as your pseudonym. Keep this brief. There is no need to explain why you are using a pseudonym.