Tooling structures to make wing/wing, fuselage/fuselage, and wing/fuselage mates have long been rather massive tools. Not only are these tools large and expensive, but they often obstruct the very drilling and fastening work to be done in the mate tool. Furthermore, these legacy mate tools can only do one job - a mate tool cannot be used for a different airplane, or even a different part of the same airplane. A flexible, more versatile system will lower the cost of aircraft with a low quantity production run planned, and a more open design can reduce the cost of assembly on a high production aircraft.This paper will discuss the development and recent breakthroughs that allow the mating of any size aircraft sections with very high precision using only a set of specialized jacks that provide six degrees-of-freedom coupled with a non-contact measurement system. Data extracted directly from a CAD 3-D model is fed into a computer system that is then used with a closed-loop control system to align the aircraft sections and/or wings in water, butt, station, roll, pitch, and yaw. The assembly area only requires a flat concrete floor capable of holding the vehicle weight. The same mate system can mate different parts of the same airplane, and be used on different production lines.This paper will explain how massive dedicated assembly tooling can be replaced by flexible assembly methods similar to the way a CNC drilling machine replaces multiple drill templates and jigs. Flexible mate and alignment systems offer huge advantages over traditional assembly monuments including lighter weight, portable, reconfigurable to multiple airframe designs, reusable, direct interface to 3-D CAD model, and best fitting aircraft segments to one another.