I guess I would try the note method first. If you can't talk to them, or you just don't get the chance, send a quick politely advising them of the issue. Most people will respond in a positive way. If they are negative, or they just don't respond, I'm afraid you will have to trim the plans yourself. It's a pain, but it may be your only choice.
If the tree is large, and you can't easily trim it, I would get your local authority involved. I have found in the past that this works, as many times these large trees, or their branches are also causing the authority problems with over head wires etc. Just my thoughts.