How to get coordinate of vertexts from CubeGeometry?

You need to make sure you understand how the vertices vector of your CubeGeometry’s sub-geometries work. Every vertex is represented by a triplet of numbers where the first represents the vertex’s x position, the second represents the y position and the third represents the z position. So if you want to get the position of the first vertex, you do this:

var x = myGeom.subGeometries[0].vertexData[0];
var y = myGeom.subGeometries[0].vertexData[1];
var z = myGeom.subGeometries[0].vertexData[2];

If you need it to be in scene space you can convert these values using the sceneTransform matrix of your Mesh.