Use bo3tools or TCEE to create bo3s.
bo3tools will allow you to 'capture' builds as bo3s in a bukkit/spigot server environment, and do fancy things like export including air (rather than ignore it), set the 'centre' block, ensure leaves are set to decay properly (useful if a tree) or include tile entities.
TCEE lets you convert schematic to bo3, there are lots of tools out there for capturing builds as schematics. TCEE really shines when you want a bo3 that is larger than a single chunk and requires multiple 'branches', if you import a large schematic and convert it, it will fill in all of the branching information for you automatically.
Alternatively, just use assets created already by the Terrain Control community, see here for a comprehensive list.
I know for trees you are spoilt for choice just going through the 350+ provided in Biome Bundle (made by myself) or the tree packs made available by @NLBlackEagle here.