If you are MTF, you must register for the selective service when you turn 18, regardless of where you are in your transition. It is still unclear if you can actually serve in the military, but you must register anyway in order to be eligible for federal jobs, federal student loans, and other federal benefits. Colleges may also check if you have been registered. You can register here: https://www.sss.gov/RegVer/wfRegistration.aspx
If you are FTM, you do not need to register for the selective service. However, if you plan to apply for college and student loans or a federal job as a male, you may be asked to prove that you are exempt from registering. You can apply for a Status Information Letter showing you are exempt here: http://www.sss.gov/PDFs/SilForm_Instructions.pdf.
For more information regarding the selective service, see this publication from the National Center for Transgender Equality.