I want to do a run but it says I must start with a fresh file.How do I get a fresh file?

You do not have to start from a fresh file for anything. You just have to start a new game. And yeah the way to remove all medals is to unfortunately delete your save data. Unless you mod your 3ds With CFW, it's the only way

Unless your doing a 100% run of the game where it is recommended but I don't think you're that far into the game to be running that