It is important to give a reader of your article a general idea what a photonic structure on your sample looks like. One very good tool for preparation of such pictures is Blender and below you can see an example of a picture prepared using this program.

A scheme of a sample created in Blender with my python script.

Blender allows you to execute a python script, which is useful in initial stages of preparations of your picture. Still, once you create a structure in Blender using a script, Blender allows you to adjust your structure by hand or to try different lighting setups, camera angles, renderers and so on.
You can find a python script producing a structure as shown in the picture above on github, here.