If I understand you correctly, you want to completely disable the default trees from the vanilla (unmodded) Minecraft game. By removing the default
Tree() lines from the config, you remove the default trees from the configs. In biomes such as Plains or Desert, which are biomes without trees, you don't have to remove a
Tree() line because there is none. You can add and modify your own if you want to spawn custom trees there, though.
Also, it would be useful if you explained your problems with a little more detail than 7 words Then we don't have to guess your problem and are we able to help you better. We cannot look in your computer, so the only information we have about your TC-troubles is the information you provide.