"No, that is not a tree."
Translation:Ne, to není strom.
When you state that something is or is not you always use TO. Regardless of gender you are describing. In fact, you do not even know a gender of what it is you are describing here. We know it is not a tree, but is it a car (neutral) or flower (feminine)? You would say the same in English. Even when talking about animate objects. No, IT is not Peter.
You would use TEN when you get to describing the object. Ne, ten není starý. = No, he/it is not old.