This work is Part II of an integrated experimental/modeling investigation of a procedure to coat nanofibers and core-clad nanostructures with thin-film materials using plasma-enhanced physical vapor deposition. In the experimental effort, electrospun polymer nanofibers are coated with aluminum materials under different operating conditions to observe changes in the coating morphology. This procedure begins with the sputtering of the coating material from a target. Part I [J. Appl. Phys. 98, 044303 (2005)] focused on the sputtering aspect and transport of the sputtered material through the reactor. That reactor level model determines the concentration field of the coating material. This field serves as input into the present species transport and deposition model for the region surrounding an individual nanofiber. The interrelationships among processing factors for the transport and deposition are investigated here from a detailed modeling approach that includes the salient physical and chemical phenomena. Solution strategies that couple continuum and atomistic models are used. At the continuum scale, transport dynamics near the nanofiber are described. At the atomic level, molecular dynamics (MD) simulations are used to study the deposition and sputtering mechanisms at the coating surface. Ion kinetic energies and fluxes are passed from the continuum sheath model to the MD simulations. These simulations calculate sputtering and sticking probabilities that in turn are used to calculate parameters for the continuum transport model. The continuum transport model leads to the definition of an evolution equation for the coating-free surface. This equation is solved using boundary perturbation and level set methods to determine the coating morphology as a function of operating conditions. (c) 2005 American Institute of Physics.