Flaherty came up with the idea of indexing Web pages that made the AltaVista search engine one of the most popular Internet search tools in the mid-1990s. Flaherty was working as a research engineer at Digital Equipment Corporation in Palo Alto when he teamed up with two other staff researchers in 1995 to develop AltaVista's technology. The Web site was made public in December 1995 and within weeks was processing several million searches a day. It was spun off from Digital Equipment as a private company in 1999. 
Member of the Marquette Chapter of Triangle Fraternity as an undergrad, where he served as chapter President. He made a habit of challenging his fraternity brothers to drinking contests that he would invariably lose; on one occasion testing the limits of human inebriation to the extent that he required gastric lavage.