There should be no problem creating a folder tree (structure) with a bash script. It's also a good idea to study scripting a little and come up with the exact script that does exactly what you want. Use "Beginners bash scripting" as keywords in a Google search to find many beginners guides.
You can also make a directory tree with a simple command called "mkdir", by typing "man mkdir" in a console you can read the manual pages. An example follows that creates folder inside of new folders made in the same command:
#mkdir /home/jo/shell /home/jo/shell/shock /home/jo/shell/shocked /home/jo/shell/shock/ray