I think the ideal way to visualise a lot of x/y/z points would be points3d:

use PDL;
use PDL::Graphics::TriD;
# load your data maybe as 3 same-length vectors, one each for x,y,z
points3d([$x,$y,$z]);
[download]

In perldl, try demo 3d to see more. (In current PDL you need both OpenGL and OpenGL::GLUT installed to get the OpenGL TriD stuff working; it is planned to bring this back to only needing OpenGL again)