Permineralized fossil coniferous woods from the Pliocene of Dunarobba, Umbria, Italy, and the Jurassic of Swindon, Wiltshire, England, were studied using non-destructive techniques on uncoated polished thin sections to elucidate their preservational history. Specimens were observed using transmitted light, polarized light, reflected light under oil, and cathodoluminescence. Selected areas were studied using a variable pressure SEM in backscattered electron mode. This allowed uncoated specimens to be examined and elemental distributions to be determined using an energy dispersive X-ray microanalyser. The data were used to interpret details of the permineralization history. Results reveal that anatomical interpretations based merely on observations of thin sections in transmitted light can be very misleading and could potentially affect the application of permineralized plant fossils, for example, in evolutionary biology, palaeoclimate analysis and isotope geochemistry.