Back in New York he established a studio and commenced work on a series of highly idealized paintings of virginal American beauties garbed in flowing classical gowns and rendered in rich, painterly oils. The works fit well within the sentiment of the times, and the paintings were eagerly bought by like-minded patrons. John Gellatly acquired twenty Thayer virgins to add to his Dewing maidens, and Charles Lang Freer purchased a generous clutch as kindred spirits to his burgeoning Whistler collection. Unlike the iconic "Gibson girl," the assertive beauty delineated by Charles D. Gibson, Thayer's damsels remained passive and quietly decorative, even when endowed with wings.

In 1901, Thayer and his family settled in Dublin, New Hampshire, with a studio in full view of Mount Monadnock. There he began a number of studies of the local landscape, employing the tonal qualities of impressionist work. He also became interested in the principles of protective coloration observed in nature, a study that would be given practical application in the camouflage techniques developed during World War I.

He was chosen to join the Ten American Painters, organized in 1897, but decided to withdraw from the group before its first show. It has been remarked that Thayer's work is now the most outmoded of any of his contemporaries. However a few years back one of the most winsome of his "angels" achieved international prominence on the cover of Time magazine.