The phrase "¡Buenos días, Manuel! ¿De dónde estás?" is mostly correct, but there's a slight issue with the use of the verb "estar." While "estás" means "you are," it is more common to ask "¿De dónde eres?" when inquiring about someone's place of origin or nationality.
The corrected phrase would be:
"¡Buenos días, Manuel! ¿De dónde eres?"
This means "Good morning, Manuel! Where are you from?" which is the appropriate way to ask