In a similar fashion to the way a customer can be made tax or fee exempt, individual orders can also be made tax or fee exempt.
This is done from the orders full detail page by selecting the show options -> edit options links and the placing a tick in the box next to fee exempt, tax exempt or both.
A tax exempt order will not have the tax rate applied, but will still be charged the environmental fee.
A fee exempt order will bypass the order minimum fee, and any delivery fees