Abstract: A real-time hotspot detection system is disclosed. In a preferred embodiment, the real-time hotspot detection system of the present invention comprises a photolithography stepper that has been modified to output z-height focus data for each cell to a fault detection module of the present invention. After the entire wafer has been exposed by the stepper, the fault detection module computes the mean and standard deviation and/or other statistical data for the wafer data and compares the computed standard deviation with a predetermined limits for “normal” standard deviation, representative of a completely flat wafer having no hotspots thereon. If the computed standard deviation is outside the limits for the normal standard deviation, the fault detection module provides control signals to the stepper for halting the operation thereof and for generating an indication to the stepper operator, via a pole light associated with the stepper, that a failure has occurred.