Barnes was selected in the fourth round of the 1996 amateur draft by the Boston Red Sox. In 1998, he was traded, along with Joe Thomas and Matt Kinney, to the Minnesota Twins for Greg Swindell and Orlando Merced. He achieved his best minor league season in 2000 with the Twins' Triple-A affiliate in Salt Lake City, winning the Pacific Coast League batting crown with a .365 average along with a 1.004 OPS, 56 extra base hits and 87 RBI. The performance earned him his first promotion to the major leagues, where he batted .351 with an .874 OPS in limited action for the Twins.

His numbers in Triple-A tailed off in 2001, and after a meager .048 average in 23 plate appearances with the 2001 Twins, he was placed on waivers and claimed by the Colorado Rockies. Barnes became a minor league nomad from there, spending the entire 2002 season with the Rockies' Triple-A Colorado Springs Sky Sox, 2003, with the Pittsburgh Pirates Triple-A Nashville Sounds. and 2004 in the Los Angeles Dodgers system with the Gulf Coast Dodgers and Las Vegas 51s.

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