You can look up the procedures for contesting an application in the Trademark Manual of Examining Procedures -- specifically section 1715, and the various subsections of that section. The particular section can be found online here:
http://www.uspto.gov/web/offices/tac/tmep/1700.htm#_Toc674575.
However, although you didn't state in your original post why you feel you own the mark that the other person is trying to register, this subsection may be relevant to your question:
"1715.01(b) Issues Inappropriate as Subject of Letter of Protest
The following are examples of issues that are not appropriate to raise in a letter of protest:
(1) A third party claims earlier common law use of a trademark but does not have a federal registration or previously-filed pending application for that mark. The ex parte examination process is limited to considering registrations and prior-pending applications. Earlier common law use, state registrations and other claims based on evidence other than federal registrations and prior-pending applications for federal registration are not appropriate for presentation to examining attorneys during ex parte examination.
(2) A third party claims that the applicant is not the proper owner of the mark. This issue requires proof that is beyond the scope of authority of an examining attorney to require during ex parte examination. In re Apple Computer, Inc., 57 USPQ2d 1823 (Comm'r Pats. 1998)."
Basically, if you feel that you own the trademark due to common-law or state law rights by virtue of prior use, you cannot raise those claims in an ex-parte letter of protest to the commissioner. Basically, if this is the case, you'll have to wait for the trademark to be granted or denied; if the trademark is granted, then you'll have to sue the trademark owner in court, and let the court sort out ownership of the mark.