I found that you need to 'unlock' the supports before you can edit the beams. An easy way to do this, goto the section you want to edit, and move the land node. Just move it a tiny bit then move back, and you should be able to edti the beams and free nodes. Also make sure you delete the all connecting beams before deleteing any free/track/land nodes.
About the trees, make sure you don't have scenery turned off in your 'grid' tab.
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