AbstractFocused ion beam (FIB) milling and lift‐out was used to prepare atom probe tomography (APT) specimens from GaN‐InGaN multi‐quantum well (MQW) nanowire arrays. Modifications to the conventional FIB lift‐out technique enable the site‐specific analysis of different regions of a single nanowire heterostructure. Three dimensional (3‐D) reconstructions of quantum wells generated by analysis along different directions with respect to the heterointerface demonstrate both the capabilities and limitations of atom probe tomographic analysis. The methods described herein can be applied to the site‐specific analysis of other complex 3‐D heterostructures. (© 2014 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)