A thin film deposition apparatus including a substrate mounting error detector, a chamber and a substrate support positioned in the chamber. The substrate support is configured to support a substrate. The substrate mounting error detector includes: a light source configured to provide a light beam to the substrate, such that the substrate reflects the light beam; a collimator configured to selectively pass at least a portion of the light beam reflected by the substrate; and an optical sensor configured to detect the at least a portion of the reflected light beam passed by the collimator. The detector is positioned and oriented to detect substrate position on a lowered support prior to raising the support into contact with an upper cover of a clamshell reactor arrangement. This configuration allows a thin film deposition process only if the substrate is correctly mounted on the substrate support. Thus, abnormal deposition due to a substrate mounting error is prevented in advance.