Hi, Welcome to JustAnswer.com, I am glad you are here! My name is Eric & I will endeavor to answer your question.
There are no regulations regarding the removal of a chimney of which I am aware or have been able to find.
You need to take it low enough below the roof to allow you room to accomplish two things.
A. You need enough room to work to structurally build any of the roof joists or trusses back which were cut out or not designed in to start with, so that you can re-sheath the roof and then tile or shingle. All to accomplish patching the hole in the roof in a structurally sound manner. For this work however, in 95% of the country, you will need a building permit to do legally.
B. It needs to be low enough to get a cap on it. A partial sheet of 1/2 cement backer board mortared in place is an acceptable cap that will never rot or be eaten by termites.
Also make sure that you do somthing with the fireplace opening below so that EVERYONE forever more, understands that this is NOT a working fireplace. You do not want house guests, or future tenants or future owners trying to start a fire in there.