Micromorphologists take small blocks of sediment intact from an archaeological site, impregnate them with resin to hold their structure in place, slice them into thin sections approximately 30 micrometers thick, and examine those sections under transmitted light and polarized light microscopes.

At this scale of observation, features that are invisible to the naked eye become apparent: the arrangement of sediment particles, the presence of biological remains (plant cells, fungal spores, bone fragments, charcoal), the chemical stains left by organic compounds, and the traces of biological activity (root channels, burrows, earthworm pedoturbation) that indicate post-depositional disturbance.

The micromorphological analysis of the Paisley Caves sediment was conducted specifically to address the stratigraphic integrity concerns raised by the critics of the 2008 paper.

The questions being asked were: do the deepest layers at the site show evidence of significant disturbance that would mix materials from different time periods?