In the Star Wars movies, we see that there is really just the Separatist Council lead by various ‘bad guys’ who are then eliminated by Darth Vader. However, in the Clone Wars series, we see that there is actually a fully fledged Senate populated by member worlds and Senators who have left the Republic. What happened to them at the end of the war? Were they told to surrender unconditionally since their droids were no longer functional?
It is unknown what became of the Separtist Senate in canon. However, in Legends, after the Separtist Council was executed on Mustafar, and Dooku and Grievous were killed, the Separtists surrendered and the senate was dissolved. A signal was sent from Mustafar by Darth Vader that shut down the Separatist Army. This all comes from the Legends Wookiepedia page here: http://starwars.wikia.com/wiki/Separatist_Parliament.