Bakufu
The structures of a han and the Bakufu were principally similar because Tokugawa Ieyasu, the founder of the bakufu, kept the governmental structure which his ancestors had developed when they were small local daimyo in Mikawa Province. Some daimyo, especially those whose ancestors had served the ancestors of the Shogun, were lords of the han and also bureaucrats of the bakufu. Most of them governed fiefs rated from one to twelve koku. Other daimyo had no permanent office in the bakufu but were appointed to a temporary office.
Each daimyo served the Shogun and received the right of governance from the Shogunate. The heir of each daimyo was recognized in advance by the Shogunate. When a son of blood or an adopted son of a daimyo was determined as the heir of his father, the son went to Chiyoda castle in Edo and met the Shogun for recognition and permission to succeed. If this procedure was ignored, the succession was cancelled by the Shogunate, and a han was abolished in a practice called toritsubushi (scrapping) in Japanese.
Though every daimyo swore loyalty to the Shogun, their relationships varied. Aside from personal factors, the relationship between each han and the bakufu was determined and influenced by the relationship between the founder of the han and the shogunate or the ancestors of the Tokugawa. Roughly there were three classifications: Shinpan (Tokugawa's relatives), Fudai (those who had been friendly to Tokugawa from before Sekigahara) and Tozama (those who were against Tokugawa at the time of Sekigahara). There was another classification by size of domain.
Read more about this topic: Han System