I can't seen to find any of these in the game. I see a research for magical trees, but that costs research scrolls. Wich I seem to need aer wood to craft. How do I obtain this aer wood if it is not spawning in my world.

Wood converts to Aer with the crucible, then wood will become Vis infused wood with the thaumic stone furnace.

Those magical trees are called Silverwood and compared to normal trees these are taller which eliminates the confusion.

Aspect machine will create one thaumic stone furnace with infused brick and Ignis. I supposed that you are after the infused wood for creating research scrolls, perhaps?