Biology utilizes energy to organize itself from the nanoscale to the macroscopic scale. We seek to determine the universal principles of organization from the molecular scale that give rise to architecture on the cellular scale. We are specifically interested in the organization of the microtubule cytoskeleton, a rigid, yet versatile network in most cell types. The microtubule network is organized by associated motor proteins and crosslinkers that are either active (use energy) or passive. The work I will present applies the ideas of statistical mechanics and condensed matter physics to the non-equilibrium pattern formation behind intracellular organization using the microtubule cytoskeleton as the building blocks. We examine these processes in a bottom-up manner by adding increasingly complex protein actors into the system. Our systematic experiments expose nature’s laws for nanoscale to micron scale organization and have large impacts on biology as well as illuminating new frontiers of active matter physics.