In this article, a methodology to extract Flash EEPROM memory contents is presented. Samples are first backside prepared to expose the tunnel oxide of floating gate transistors. Then, a Scanning Electron Microscope (SEM) in the so called Passive Voltage Contrast (PVC) mode allows distinguishing ‘0’ and ‘1’ bit values stored in individual memory cell. Using SEM operator-free acquisition and standard image processing technique we demonstrate the possible automating of such technique over a full memory. The presented fast, efficient and low cost technique is successfully implemented on 0.35$\mu m$ technology node microcontrollers and on a 0.21$\mu m$ smart card type integrated circuit. The technique is at least two orders of magnitude faster than state-of-the-art Scanning Probe Microscopy (SPM) methods. Without adequate protection an adversary could obtain the full memory array content within minutes. The technique is a first step for reverse engineering secure embedded systems.