Scanning electron microscopy works by shooting a narrow beam of electrons at a specimen. When the electrons hit the specimen, some electrons are scattered straight back towards the beam (backscatter electrons) and others are knocked loose from the sample (secondary electrons). The electron beam can be scanned over the surface of the sample and the intensity of the backscatter and secondary electrons measured with appropriate detectors. By scanning the beam in a raster pattern, a picture of surface can be constructed. This process would not work in air because the electrons we are detecting would be scattered by gas molecules, so the sample must be placed in a vacuum chamber and almost all the air pumped out of the chamber before we can get acceptable images. The high vacuum required in the chamber has been a problem for wet or moisture-containing specimens (e.g., natural organic materials like textile, leather, and wood) since pumping the air out of the chamber encourages the water in the specimens to evaporate and then the specimens warp and crack while under examination. Another problem has been the necessity for the specimen to be conductive (otherwise electrons accumulate on the specimen and 'white out' the signal we are trying to detect) so we have usually had to coat organic specimens with a fine layer of either carbon or gold. Recent advances in SEM technology have allowed 'environmental' chambers which do not need such a high vacuum to function and, because there is a little air and water in the chamber, clever modifications to the detector ensure that electron accumulation on the specimen is less of a problem. The Field Museum has a 50 cm diameter environmental chamber which allows us to examine a 25 cm diameter object without coating.

Interaction between the electron beam and the sample also generates soft x-rays which can be analyzed using Energy Dispersive X-ray Spectroscopy (EDS or EDX). The Field Museum's SEM is equipped with an EDS detector which allows us to quantify the chemical elements present at the surface of a sample.