I'm going to set the tone with a little factoid: there's another thread near this one where the community assistants verify that Molecule Manipulation can cause death via freezing of blood. That's * metal.
From what I understand, Molecule Manipulation refers to the character having direct control over the state of molecules in a chemical regardless of state. The limitations for this would be what you'd expect from something of that sounding - your character isn't a high-powered magnifying glass, so for 90% of the time interaction is based on energy level (adding or removal, but cannot cause explosions), pressure, and to an extent structure and state (gaseous air becomes solid, forming a defensive barrier). This causes mental fatigue and stress on the character, signature with nosebleeds as a given side effect.
As for ripping off part of a tree and re-purposing it, that's something I was going to start doing later on with 'Dwelly to slap Dottie once. The problem with actually restructuring the molecules of the tree is that, unlike with broad applications such as "add a little bit of heat," your character would need to know the exact chemical compound of the tree sample in order to more finely manipulate it, and even then you'll be pushing the extent of the power before its cost in concentration does something like black you out. If the tree had a melting point, you could try to reach it to liquefy it, but I don't care to google how hot a tree needs to be before it melts.
Just my 2 cents