As well as hydrographic surveying, Thomas carried out important work on the archaeology of the northern and western isles.
[6] He authored several papers on this work, from 1851, including a plan of the barrows, standing stones and other structures around Stenness, Orkney (Thomas, 1851) which was the first detailed survey of this area;[7]: 38 and descriptions of buildings such as black houses, beehive houses and brochs in the Outer Hebrides (Thomas, 1862, 1890).
His specimens are frequently referred to in the major works on zoophytes by Johnston (1847)[9] and on molluscs by Forbes and Hanley (1853)[10] and Jeffreys (1869).
He noted that some of the beehive houses in Lewis and Harris were still in use as dwellings for the summer pastures, whereas elsewhere in Scotland and Ireland such buildings had been abandoned or were only used for storage.
He described the living arrangements in these houses, as well as recounting legends associated with them, such as that of the shape-shifting Each-uisge or water horse (Thomas, 1862).
In 1863, in the company of fellow antiquarian Arthur Mitchell on Lewis, he met a stone-breaker eating out of a traditional unglazed earthenware pot, and they investigated the making and use of these vessels, known as craggans.
Frances saw there could be a demand for woollen goods on the mainland, and first promoted knitted stockings, and then together with Lady Dunmore, developed a market for Harris Tweed.