If my husband and I have been separated for 6 years now, he is prison, how can I file for a divorce?

You don't indicate whether you have children together or own and property together, but you should generally be able to file for divorce where you last lived together as husband and wife, or possibly where you are now living if not in the same place as before, and serve him with the papers in prison. Consult with an attorney to discuss the specifics of your situation and your options.

How? In writing, by filing a petition for dissolution of marriage, and then having it served upon him.

If you are in Florida file the usual paperwork, in the Petition indicate you are separated for 6 years due to his being in Prison. The clerk of Court will issue a Summons, the prison will have a procedure in place for him to be served the papers. Once he is served procedure is the same for all matters.