Systems and methods for reducing alteration of a specimen during by charged particle based and other measurements systems are provided. One system configured to reduce alteration of a specimen during analysis includes a vacuum chamber in which the specimen is disposed during the analysis and an element disposed within the vacuum chamber. A surface of the element is cooled such that molecules in the vacuum chamber are adsorbed onto the surface and cannot cause alteration of a characteristic of the specimen during the analysis. One system configured to analyze a specimen includes an analysis subsystem configured to analyze the specimen while the specimen is disposed in a vacuum chamber and an element disposed within the vacuum chamber. A surface of the element is cooled such that molecules in the vacuum chamber are adsorbed onto the surface and cannot cause alteration of a characteristic of the specimen during the analysis.