changing or removing the Headers and Footers from mailing templates
Possibly I don't follow the question, but using CiviMail you can avoid the need for using Headers or Footers by ensuring that you include all the required tokens in the template itself. You can also 'edit' the existing default Header and Footer and set them to not be default, hence when you then use your template in CiviMail, no header or footer will be automatically included, and none will be required.