Courtesy of the National Center for Transgender Equality, here is an informative PDF document that answers frequently asked questions regarding airport whole body scanning and how it relates to trans travelers.

• If you are one of the unlucky few chosen for special treatment, you have the right to choose whether TSA scans you or pats you down, both are intrusive
• Consider packing your binding and prosthetic devices in your luggage to avoid increased scrutiny and delay. Also place your syringes, liquids, gels and powders in your checked baggage.
• You have the right to be treated respectfully without discrimination. If this right is violated you should file a complaint with the Department of Homeland Security Office for Civil Rights and Civil Liberties as soon as possible.