There could be two ways to register the pen-name. First could be protection under copyright. The literary work is protected under copyright in legal name of the author. In the same application, you can enter your pseudonym in appropriate field for protection.
On the other hand, there can be another a trademark registered. Generally, the trademark is not allowed unless it is associated with particular goods or services such as a blog, book, comic series, etc.
You need to understand the legalities of both kind of protection with an attorney prior to any decision. If you need help, consult an attorney at LegalWiz.in