To ask where your doctor is from, you would typically use the formal "vous" form. Therefore, the best option from your list would be:
D'où venez-vous?
This phrase means "Where are you from?" in a formal or polite context. If you have a closer relationship with your doctor and are on informal terms, you might also use:
D'où viens-tu?
This means "Where are you from?" in a more casual context. However, in a professional setting, it's better to use the formal version.