This paper deals primarily with the difficulties and solutions to scanning transmission electron microscope (STEM) sample preparation by dual beam focused ion beam. Approximately twenty major challenges were encountered spanning hardware, software, and material sample preparation. The main focus is upon the variety of challenges which are encountered in trying to implement automated STEM and TEM sample fabrication with minimal operator input and the engineering solutions implemented to overcome these challenges. The automated STEM script has evolved significantly from the first generation attempt and is described in more detail in this paper. The mechanical, software, and materials challenges encountered are also presented. The paper highlights a mechanical issue with the ion aperture motor mechanism, which required extensive troubleshooting to fully diagnose and correct. A long standing software routine had to be modified to fully enable script automation by extending the beam dwell time of the automatic brightness contrast routine.