If you want to simulate the entire device of 2 microns, you need to use TCAD tools that are designed to study devices at the macroscopic level in the continuum approximation. VNL-ATK is meant for atomistic modeling of devices at the microscopic level.
VNL-ATK can, however, be used to extract microscopic, material-specific parameters for TCAD models that adopt this kind of parameters as input. You may also construct and visualize a nanoscaled device in VNL-ATK, e.g., a quantum dot attached to electrodes, and then calculate IV characteristics or other properties of this kind of nanodevices.