A Not Guilty plea can be entered with the court any number of ways.  They are as follows:  in person, by telephone, by e-mail, by fax or by regular mail.  You should have your summons # or complaint # available when entering your plea.  However, not all Not Guilty pleas can be entered this way.  For instance, a Not Guilty plea for a matter of consequence requires an arraignment.  For this situation, the Not Guilty plea is entered on the day of your arriagnment with the Judge, unless a Not Guilty plea is entered by an attorney on your behalf.