Measurement of retinal nerve fiber layer (RNFL) thickness using optical coherence tomography (OCT) is commonly used in the detection and management of glaucoma. The Stratus OCT (Carl Zeiss Meditec, Inc., Dublin, CA) is widely used, but image acquisition is subject to artifacts, such as those caused by normal fixational eye movements, and this leads to unreliable measurements. Novel analytical methods have been developed to estimate the amount of misalignment of the circular scanning protocol used by the Stratus OCT. A computer program with a graphical user interface implementing these methods has been written by some of the authors. A case example is presented in this report that shows the effect that vertical displacements of the OCT scan have on measured RNFL thickness. The example is used to demonstrate how the software can be used for estimating the positional alignment of the scan circle. This software can potentially improve the identification of unreliable RNFL thickness measurements and is freely available from the authors.