In the present invention, a product is manufactured in a manufacturing process controlled and tracked using a manufacturing execution system or MES. An engineering change is made to the product specification while units of the product are in the manufacturing process. The product unit is reworked to match the changed specification. The engineering change implementation function of the manufacturing execution system identifies the products units to be reworked, provides instructions for the rework, and tracks that all affected product units are reworked to the changed specification.