Yes, the clear seeds are chaff (empty seed). With a good light behind, typical viable lily seeds have visible endosperm and embryos, similar to this:
The embryos are the lines in the center parts of the seeds.
Many of us make it a practice to plant the chaff anyway, however. Sometimes the embryo hides or is infinitesimally small, and it is missed. With my ten years of lily seed planting experience, I do discard most of the chaff material, but anything that may have the slightest possibility of being viable, I plant. Using a light box or a flashlight app on your phone is a great way to employ the backlighting needed to determine possible viability of lily seed.
