A method of removing an out-of-tolerance area in a composite structure comprises determining the location of the out-of-tolerance area and selecting a volume of the composite structure to be removed based on the location of the out-of-tolerance area. The method may further include programming a machine tool to remove the volume and to pause after removal of each one of a quantity of layers of the volume. The method may additionally include removing one of the layers using the programmed machine tool. The method may further include restoring the volume removed using the programmed area removal digital definition.