Methods of doping nanostructures, such as nanowires, are disclosed. The methods provide a variety of approaches for improving existing methods of doping nanostructures. The embodiments include the use of a sacrificial layer to promote uniform dopant distribution within a nanostructure during post-nanostructure synthesis doping. In another embodiment, a high temperature environment is used to anneal nanostructure damage when high energy ion implantation is used. In another embodiment rapid thermal annealing is used to drive dopants from a dopant layer on a nanostructure into the nanostructure. In another embodiment a method for doping nanowires on a plastic substrate is provided that includes depositing a dielectric stack on a plastic substrate to protect the plastic substrate from damage during the doping process. An embodiment is also provided that includes selectively using high concentrations of dopant materials at various times in synthesizing nanostructures to realize novel crystallographic structures within the resulting nanostructure.