The ciliates are the only organism with micronuclei and macronuclei. Ciliates are unicellular but have a very complicated cell.
Cilia are structurally the same as flagella and are actually short flagella.
The name cilia was coined prior to knowing that they are flagella and the name has stuck. These are organisms that have cilia. Cilia are short flagella. Ciliates have micronuclei and macronuclei. The micronuclei are involved reproduction.