Methods and systems for determining focus settings for use in a specimen scan are provided. One method includes generating a focus map defined as values of best focus as a function of position on a specimen using output generated in one or more pre-focus swaths scanned on the specimen by an output acquisition subsystem configured to direct energy to a specimen, to detect energy from the specimen, and to generate output responsive to the detected energy. The method also includes interpolating the focus map to generate focus settings for a scan performed on the specimen during a process and storing information for the generated focus settings for use in the scan performed on the specimen during the process.