The great place to start would be by answering yourself the following questions: What does the band structure diagram show? What is on x and y axes? Where is the Fermi level? What specific questions do you want to address by looking at the band structure?

You need to supply high-symmetry points according to your system. Scaling indefinite range is important to interpret the diagram. gnuplot needs some scripting skills, I recommend xmgrace for GUI support.

If "Bandstructure" is defined in the usual way, it really applies only for periodic solids, not for molecules.