This paper deals primarily with the difficulties and solutions to STEM sample preparation. The dual beam focused ion beam (DBFIB) whole wafer platforms often come with scripting features which allow the tool to operate with a high level of automation. The main focus of the paper is on 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 the challenges. The paper demonstrates that the challenges with making STEM and TEM samples in a highly automated fashion by DBFIB, while difficult, are not insurmountable. It has highlighted 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.