Systems and methods for repairing defects on a specimen are provided. A method may include processing a specimen, detecting defects on the specimen, and repairing one or more of the defects. An additional method may include detecting defects on a specimen, repairing one or more of the defects, and inspecting the specimen to detect defects remaining on the specimen subsequent to repair. A system may include a process chamber, a measurement device configured to detect defects on a specimen, and a repair tool configured to repair one or more of the defects detected on the specimen. An additional system may include a measurement device, a repair tool, and an inspection tool configured to detect defects remaining on the specimen subsequent to repair. The systems may also include a processor configured to alter a parameter of an instrument coupled to the repair tool in response to output from the measurement device.