A method of handling integrated circuit dies with defects is provided. After forming a plurality of dies on one or more silicon wafers, test equipment may be used to identify defects on the dies and to create corresponding defect maps. The defect maps can be combined to form an aggregate defect map. Circuit design tools may create keep-out zones from the aggregate defect map and run learning experiments on each die, while respecting the keep-out zones, to compute design metrics. The circuit design tools may further create larger keep-out zones and run additional learning experiments on each die while respecting the larger keep-out zones to compute additional design metrics. The dies can be binned into different Stock Keeping Units (SKUs) based on one or more of the computed design metrics. Circuit design tools automatically respect the keep-out regions for these dies to program them correctly in the field.