Remove the caps from the lens case, then cut a small slot in each bowl (see the second picture). The amount of material you need to remove will depend on the size and design of the "handle" portion of your ear buds. The last image in the Instructable shows some white buds that needed a longer thinner slot than the black ones. The slot should be big enough to allow the bud to rest entirely in the bowl of the lens case. If it rises above the lip of the bowl, then the caps will not screw on properly.
The easiest way to cut the cases is to heat an exacto knife in flame. If you don't use heat then use a very sharp blade and go slow. The plastic is a little brittle and is prone splitting if you apply too much pressure.