Normally one resigns as an officer and/or director of a nonprofit corporation by submitting a letter of resignation (today probably an email) to “the corporation.”  Check your bylaws to see if it spells out the procedure.  If they don’t designate a specific recipient of the letter, you could give it to the board chair, if someone other than yourself, the secretary, or the second in command.  Or you might want to send it simultaneously to all of the other officers or to the entire board.  It should state the time at which you want it to be effective, either upon receipt or some later date which might give an opportunity for an orderly transition.

Your responsibilities will cease upon the effective date of the resignation, which may or may not be exactly when you tender it.  You could conceivably be liable for improper actions prior to the resignation, but it is not likely that you would incur any new liability.  You should not have any responsibilities thereafter that you don’t specifically accept.

You probably can’t remove your name from filings with the Secretary of State because those filings state the facts at a specific point in time, when you were actually involved.  The best you can hope for is that your successors will not list your name improperly when they have to make the next filing.