The disclosed embodiments include a system and method for manufacturing an integrated computational element (ICE) core. The method comprises varying a distance between a thermal component relative to a substrate holder that holds at least one substrate during a thin film deposition process to improve uniformity of the ICE core. In one embodiment, varying the distance between the thermal component relative to the substrate holder that holds at least one substrate includes moving at least a portion of the substrate holder in at least one direction relative to the thermal component and also moving the thermal component in at least one direction relative to the substrate holder during the thin film deposition process.