Liffiton began his junior career with Aylmer Blues in the OHA-B before he was selected in the 16th round, 326th overall, in the 2000 Ontario Hockey League priority selection by the Plymouth Whalers. Joining the Whalers in the 2001–02 season, and developing as a physical stay-at-home defenseman, Liffiton recorded his best season statistically in 2002–03 with 5 goals for 16 points in 64 games to help the Whalers reach Western Conference finals against the Kitchener Rangers. He was subsequently drafted 63rd overall in the 2003 NHL Entry Draft by the Colorado Avalanche. In his final year with Plymouth in 2003–04, Liffiton's rights were included in a trade by the Avalanche, along with Chris McAllister, to the New York Rangers in exchange for Matthew Barnaby and a third round selection in 2004 (Denis Parshin) on March 8, 2004.