In the past a good way to separate mothers from infants was water. I suspect in recent versions mother infant-recovery has been improved, or perhaps infants can swim, because my swimming pools haven't seemed to accumulate infants.
If you just want to smish the kiddies though that's much easier, kiddies are very easy to lure to their deaths. Here is an example of how to do it:
Build a room.
Pave the floor of the room with constructed floors - as many floors as you want dead children.
Occupy all the adults with a big hauling job and then immediately designate the floors to be deconstructed.
Kiddies will run into the room and start deconstructing floors.
Lock door, and fill room with water (or anything else which will be lethal to kiddies).
There are really a lot of variants on this theme, for example, you could have a bridge over magma, with constructed walls, have the kiddies de-construct walls then open the bridge, or lower a bridge on them, or whatever.
However I have not tested this method in this version, it relies on some dubious behaviour that Toady will probably fix one day.
I imagine you could also make a fully automated kiddy-grinder in the following way:
Use a standard 'one-way' hatch which triggers for adults but not children, that is have a pressure plate set to be triggered by anything over half the weight of a dwarf, the pressure plate is linked to a hatch over space - might need to use hatches plural to prevent jumping! Also smooth walls to prevent climbing. The hatch should be next to the pressure plate. So when an adult comes along and steps on the plate he'll be turned around by the hatch opening, but a kiddy being too light to trigger can run over the plate, across the hatch(es) into the maws of waiting death (whatever you like really). Use a meeting zone as kiddy bait. This'll also grind your animals and pets if they are light enough, and aren't pastured/chained.
There have been a lot of changes in recent versions, so these methods may not work.