Fernando Perez rehabbed with the Stone Crabs for three games during the 2009 season. During his assignment, he was 2 for 10 with two stolen bases.
Perez was drafted by the Devil Rays in the seventh round of the 2004 draft out of Columbia University. He made his pro debut for the Hudson Valley Renegades in 2004. He worked his way through the organization, playing for Southwest Michigan Devil Rays in 2005, Visalia Oaks in 2006 and Montgomery Biscuits in 2007. He made major league status in 2008 when he began the season with the Durham Bulls and enjoyed a call-up to the Rays. Injury struck in 2009, sending Perez to the Stone Crabs and GCL Rays for rehab before returning to the big club.
Perez spent the entire 2010 season with the Durham Bulls. Following the season, Perez was a member of an eight player trade with the Cubs that sent him along with Matt Garza and Zach Rosscup to the Cubs.