In this work, we report on numerical simulations of electron transport through three-dimensional (3D) quantum structures in both linear and nonlinear response regimes of transport. The structures considered include 3D quantum point contacts, quantum dot structures, quantum dot superlattices, and resonant tunneling structures. The simulations are done using scattering matrix method. For 3D quantum point contacts, the linear response conductance shows quantizations in units of 2e2/h, but conductance steps can be in multiples of 2e2/h. The resonant tunneling peaks are found in the conductance spectra for both the quantum dot structures and resonant tunneling structures. The linear response conductance of 3D quantum dot superlattices shows multiple-fold splittings, reflecting the formation of energy minibands in the systems. By examining the dependence of peak positions on the distance between barriers, the correspondence between resonant tunneling peaks and resonant states is determined. When a small but finite source-drain voltage is applied, the nonlinear conductance is found to be asymmetric for an asymmetric 3D quantum point contact.