Current S/TEM automation requires highly trained microscopists to build specialized acquisition and analysis recipes for specific semiconductor structures. Recipes can be challenging to write and take a long time, therefore the industry continues to rely on manual operation to overcome TEM analysis demands. Time to develop robust automation is often too slow for the product change rate of industry development cycle. To overcome this barrier, Smart Automation was developed on a Thermo Scientific Metrios TM AX 200kV S/TEM as an application providing a generalized acquisition workflow that is ready to use without requiring specialist intervention. The application interacts with a Fully Convolutional Neural Network (FCN) through a user-friendly interface for navigation and auto alignments. The FCN is the key enabler for lowering the bar to automation set up with a time to robust automation within hours instead of days.