A method and apparatus for machining a part for an assembly. First sensor data is acquired for a surface of a first part from a first sensor system. Second sensor data is acquired for a set of existing holes in a second part from a second sensor system. A surface model of the surface of the first part is generated using the first sensor data. First offset data is computed based on a nominal model of a third part that is nominally positioned relative to the surface model within a three-dimensional virtual environment. Second offset data is computed for the set of existing holes using the second sensor data. Overall offset data is generated using the first and second offset data, wherein the overall offset data is used to drill a set of holes in the third part for use in fastening the third part to the second part.