This paper presents significant new developments concerning the full band, quantum simulation of nanostructured systems and nanoscale electron devices based on an empirical pseudopotential Hamiltonian. We demonstrate that the method is of general applicability, in fact we show results for planar, ultra-thin body FETs and also for three-dimensional, nanowire FETs, we deal with different crystal orientations and account for possible stress/strain conditions in the simulated systems. Some of the simulations reported in this paper have been made computationally viable by the substantial improvements of the numerical efficiency compared to our previous pseudopotentials based methodology.Most of the methods and algorithms discussed in this paper are not specific to an empirical pseudopotential Hamiltonian, on the contrary they can be applied also to different Hamiltonians described with a plane waves basis, which are frequently employed for ab-initio, Density Functional Theory based calculations. The application of the methodologies described in this work may thus be more far reaching than it is illustrated by the case studies explicitly addressed in the present paper.