After “Home Improvement,” Thomas did continue to work, as shown on his IMDb page. In 2000, he made an appearance on an episode of the third season of “Ally McBeal” called “Do You Wanna Dance?” as an underage boy that Ally (Callista Flockhart) has apparently been chatting with online without realizing it (via TV Maze). That same year, he voiced the character of Tyler Tucker on “The Wild Thornberrys.” Additionally, he made guest appearances on shows like “Smallville,” “The Simpsons,” “8 Simple Rules” and “Veronica Mars” all the way through 2005.
At that point in his life, Thomas also expressed an interest in directing for the first time. In 2006, he directed a short called “The Extra.” However, after that, he disappeared for some time. He doesn’t have any social media accounts, so fans really had no way of finding out what he was doing. And clearly, this is exactly what he wanted.
“I never took the fame too seriously,” he told People in 2013. “It was a great period in my life, but it doesn’t define me. When I think back on the time, I look at it with a wink. I focus on the good moments I had, not that I was on a lot of magazine covers.”
His non-Hollywood activities during the 2000s were likely college-related, though. According to Showbiz Cheat Sheet, he graduated from Chaminade College Preparatory School in 2000. Thomas then attended Harvard University, St. Andrews University as a contemporary of Prince William and Kate Middleton in 2002 (via The Scotsman), and Columbia University. He is listed as a 2010 graduate of Columbia.