Medicare Choices Empowerment and Protection Act - Amends part B (Supplementary Medical Insurance) of title XVIII (Medicare) of the Social Security Act to direct the Secretary of Health and Human Services (HHS) to: (1) establish an Advance Directive Certification Program to encourage eligible beneficiaries to adopt and maintain certified advance directives to guide the delivery of health care to them, and (2) make a one-time payment (of $50 for using a manual process, of $75 for using on-line processes only) to each eligible beneficiary that adopts a certified advance directive and registers it with the Program.