Does Migration from old Mac to new, also transfer the folder structure?

I have successfully used Migration Assistant to set up a new Mac several times. In every instance the new computer was set up with everything looking the same and being in the same places. So, the answer is yes.

When you initially set up Migration Assistant it will ask you where you wish to easter (1) your preferences and settings, (2) your applications and (3) all of your files. Each category is all or nothing. If you only wish to transfer some files, answer no. Then you can manually copy those files over later.