Wait until the plantlets have a bit of rhizome and some roots of their own, then pluck them off.
Java Fern (and Anubias and Bolbitis and a couple others less commonly seen) are rhizome plants - don't bury the rhizome in sand or gravel, you stand a good chance of killing them if you do. Instead, use cotton thread or florist's wire to tie the rhizome to a small rock, place the rock on the substrate.
Interesting (and maybe important for you) side note - those plantlets you are seeing are a defensive mechanism of Java Ferns. When the plant feels threatened, it produces them so that when the leaves die, babies float downstream to a new and hopefully better location than the mother plant had.
This come from mainly two things - it is often seen in heavily shaded or low light situations (In nature, it would signify an area becoming overgrown and limiting the plant, hence send babies downstream), and also seen when you are killing a rhizome via burying it. I'm hoping your mother plant's rhizome isn't buried in sand?
