Research is important. Read up on real - life samurai history and traditions to add authenticity to your fanfiction. Also, study how the Naruto series builds its world, from the different villages to the power systems. Incorporate your own ideas into this framework. For instance, you could create a new type of jutsu inspired by samurai techniques.
First, you need to have a solid understanding of both the Naruto universe and the samurai concept. Then, create unique characters that blend the traits of samurai and ninja. For example, a character who values honor like a samurai but has ninja - like stealth.