Select some vertices from GeometryBuffer

Hello, community.

I created some sort of a 2D map on a GeometryBuffer object (used z = 0)

And I need to select some of the points (vertices) on that map. I try to use a SelectionBox from example (three.js examples), but it returns only whole GeometryBuffer object.

Is that any ways to select only some points from that object?
Or I need to use another objects or create separated objects for each point? I think about it, but I want to put more than 100-300k points at scene, but I think it will be really bad for performance