We consider the front, back, and sides of a tree to be relative to our imagined or real viewpoint. In your case, this will depend on descriptions of the event in the story so far.
He stopped in front of the tree, makes me imagine that he is facing the tree - maybe closely examining the bark?
He stopped with his back to the tree, sounds as though he is making a last stand against a pursuer.
He stopped next to the tree, brings me a mental picture of him standing to one side of the tree, from the point of view of someone watching him run.
Please can you say (possibly with a diagram) what exactly it is that you want it to mean?