"But that is not a tree."
Translation:Ale to není strom.
That, this, It is - to je or je to (irrespective of the gender).
The sort of sentence you propose makes sense when speaking about something already discussed and mostly just about people. On(a) není hlupák. (S)he is not a dumb person. For nonliving entities it makes more sence just with adjectives. Ono není velké. It is not big. It should closely followw the sentence where that he she or it was already specified.
Viděls naše auto? Ono není velké(, ale je dobré). Have you seen our car? It is not big(, but it is good.)
With a noun it still leads to "je to".
Viděls naše auto? Není to BMW, ale je dobré. Have you seen our car? It is not a BMW, but it is good.