A method for improving the measurement of semiconductor wafers is disclosed. In the past, the repeatability of measurements was adversely affected due to the unpredictable growth of a layer of contamination over the intentionally deposited dielectric layers. Repeatability can be enhanced by removing this contamination layer prior to measurement. This contamination layer can be effectively removed in a non-destructive fashion by subjecting the wafer to a cleaning step. In one embodiment, the cleaning is performed by exposing the wafer to microwave radiation. Alternatively, the wafer can be cleaned with a radiant heat source. These two cleaning modalities can be use alone or in combinationn with each other or in combination with other cleaning modalities. The cleaning step may be carried out in air, an inert atmosphere or a vacuum. Once the cleaning has been performed, the wafer can be measured using any number of known optical measurement systems.