Well, I assume you mean that you are looking for those three classes inside the org.eclipse.m2m.atl.engine package ....
What I can tell you is that I use Eclipse Helios SR2 (Modeling package) which is related with ATL 3.1.2.
Under that environment, you can find the classes AtlLauncher and AtlModelHandler inside the package org.eclipse.m2m.atl.engine.vm which is in turn inside the org.eclipse.m2m.atl.engine.vm_3.1.2.v20110119-0755.jar
The class AtlEMFModelHandler is inside the org.eclipse.m2m.atl.drivers.emf4atl package which in turn is inside the org.eclipse.m2m.atl.drivers.emf4atl_3.1.2.v20110119-0755.jar
Those jars should be present inside the plugins folder.