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Outside of gender, you cannot customize the look of Fire Emblem: Three Houses' protagonist
One default face for each
Byleth is the main character in Fire Emblem: Three Houses. At the start of the game, you'll be able to pick between a male or female character, but that's it. Nintendo has confirmed to USGamer that there will be no visual customization for the player character after that.
"Although you can choose Byleth's gender and, of course, assign character skill sets, the actual avatar is not customizable in terms of look."
[Link]