Line annotations can be added directly to a figure. For example, this code adds a couple of lines to divide a figure into 4 squares:
f=figure;
annotation('line', [0 1], [0.5 0.5]);
annotation('line', [0.5 0.5], [0 1]);
See the help for ANNOTATION to inspect the different types of annotations you can add.
You might also consider laying out your GUI with uipanels, which can have visible borders and can be a good way to contain graphics.
