As far as I know Accusative case is used for objects (I sure do hope I am using the proper term, as English is not my first language) and the Instrumental case is used for the tool with which the action is performed.
But what happens if the tool is the object?
I am writing with a pen.
Я пишу ручкой.
I am not sure if the sentence in Russian is correct, but either way - is pen/ручка in Accusative or Instrumental case?