Methods and systems for preparing a sample for thin film analysis are provided. One system includes an energy beam source configured to generate an energy beam. The system also includes an energy beam delivery subsystem configured to direct the energy beam to a sample and to modify the energy beam such that the energy beam has a substantially flat-top profile on the sample. The energy beam removes a portion of a contaminant layer on the sample to expose an analysis area of a thin film on the sample. One method includes generating an energy beam and modifying the energy beam such that the energy beam has a substantially flat-top profile. The method also includes directing the energy beam to a sample. The energy beam removes a portion of a contaminant layer on the sample to expose an analysis area of a thin film on the sample.