Ok so I got my model for 3ds max into the msh viewer and the leaves on my tree are white, and they are see though on one side. The bark is working fine on the tree but just the leaves. Did I setup the transparency map wrong because it was working fine in Max.

If someone can tell me how to fix or where I messed up that would be a lot of help.

You have to hex edit transparency on the particular material that is supposed to have it, and then have the alpha map in the alpha channel of the texture. There are various threads on this subject, just look in the various FAQ threads at the top of each forum.