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The United States Medical Licensing Examination (USMLE) Step 3 examination includes a computer-based case simulation component where examinees iteratively manage a simulated patient by placing various order of actions while receiving patient status feedback through a graphical user interface. In this study, we analyzed sequence data from a single CCS case to facilitate an understanding of medical graduates’ clinical reasoning processes. Due to the nonstandard format of the sequence data, we applied a bottom-up data-driven approach utilizing multidimensional scaling to extract features based on the relative differences among examinee sequences. Results suggest that the extracted features could provide additional information related to Step 3 competencies and differences between US/Canadian and international medical school graduates.