Graphics like Towns and Gnomoria

I am interested in making a java game with graphics like Towns or Gnomoria. I know how to make it so that I had top down tile based graphics like Dwarf Fortress but I am unsure how to make 2.5d graphics like Towns. I have some slight ideas on how to make a top down isometric view but I am unsure how to draw multi z-level graphics in an isometric view. Any advice or good tutorials for me to look at? I could use any help you are willing to give.