Central to the bottom-up paradigm of nanoscience, which could lead to entirely new and highly integrated functional nanosystems, is the development of effective assembly methods that enable hierarchical organization of nanoscale building blocks over large areas. Semiconductor nanowires (NWs) represent one of the most powerful and versatile classes of synthetically tunable nanoscale building blocks for studies of the fundamental physical properties of nanostructures and the assembly of a wide range of functional nanoscale systems. In this article, we review several key advances in the recent development of general assembly approaches for organizing semiconductor NW building blocks into designed architectures, and the further integration of ordered structures to construct functional NW device arrays. We first introduce a series of rational assembly strategies to organize NWs into hierarchically ordered structures, with a focus on the blown bubble film (BBF) technique and chemically driven assembly. Next, we discuss significant advances in building integrated nano electronic systems based on the reproducible assembly of scalable NW crossbar arrays, such as high-density memory arrays and logic structures. Lastly, we describe unique applications of assembled NW device arrays for studying functional nanoelectronic-biological inter faces by building well-defined NW-cell/tissue hybrid junctions, including the highly integrated NW-neuron interface and the multiplexed, flexible NW-heart tissue interface.