distinguishing different polymer strips on a flat surface

I'm trying to dissolve down into a thin layer of polymer that is spread on a surface, so that I may reveal a second polymer, and have them be at the same level. Here's a picture of what I mean:

My problem is, I can't tell if I'm all the way through the first/topmost polymer layer or when I hit the second/bottommost polymer bars. I'm using a fluorescent/light microscope, and I'm wondering if there is some kind of dye or coating that can be used? Or is it some more complicated piece of equipment that uses infared or AFM? Thanks in advance!

Dye the matrix, or dye the lumps, or coat the lumps with a dyed coating beforehand. Or if the polymers have two different surface energies, you could detect the exposure of the lumps by drawing with an appropriate surface energy pen or liquid. I'm slightly surprised that it's so difficult to tell the difference optically- are the polymers similar refractive indices?