The scanning electron microscope (SEM) has gone through a tremendous evolution to become a critical tool for many and diverse scientific and industrial applications. The improvements that have been made have significantly improved the overall SEM performance and have made the instrument far easier to operate. But, ease of operation also fosters operator complacency. In addition, the user friendliness has reduced the “apparent” need for more thorough operator training for using of these instruments. Therefore, this overall attitude has fostered the concept that the SEM is just another expensive digital camera or another peripheral device for a computer. Hence, a person using the instrument may be lulled into thinking that all of the potential pitfalls have been eliminated and they believe everything they see on the micrograph is always correct. But, this may not be the case. The first paper in this series, discussed some of the issues related to signal generation in the SEM, instrument calibration, electron beam interactions and the need for physics-based modelling to accurately understand the actual image formation mechanisms. All these were summed together in a discussion of how these issues effect measurements made with the instrument. This second paper, discusses another major issue confronting the microscopist: specimen contamination. Over the years, NIST has done a great deal of research into the issue of sample contamination and its removal and elimination and some of this work is reviewed and discussed here.