Puffer was drafted by the Minnesota Twins in the 27th round of the 1994 Major League Baseball draft and played two seasons for their Gulf Coast League affiliate before being released. On May 28, , Puffer signed with the California Angels, playing two seasons for them before his release on December 15, . He signed with the Cincinnati Reds on January 14, , and played as high as Double-A before becoming a free agent after the season; he had an ERA of 1.99 in 63.1 innings with Clinton in 1999. On November 18, 1999, he signed with the Colorado Rockies, but was released on May 18, .