After not playing in a game in 2004, Molleken spent 2005 again with the GCL Pirates, allowing 24 runs in 30.0 innings of work.

In 2006, Molleken spent the season in Low-A ball with the Williamsport Crosscutters, pitching to a 2.51 ERA with 22 strikeouts in 13 games.

He split the 2007 season between three affiliates, the Low-A State College Spikes, the Single-A Hickory Crawdads, and the High-A Lynchburg Hillcats, accumulating a 3.92 ERA with 44 strikeouts in 39.0 innings for the three teams.

He split the 2010 season between the Triple-A Colorado Springs Sky Sox and the Double-A Tulsa Drillers, pitching to a cumulative 5.05 ERA in 36 appearances.

On November 14, 2011, Molleken re-signed with the Rockies on a minor league contract that included an invitation to Spring Training.

[2][3] He spent the year in Colorado Springs, and pitched to a 3-0 record and 5.18 ERA before being released to pursue an opportunity in Japan.

[1] On July 22, 2013, Molleken signed a minor league contract with the Milwaukee Brewers organization was assigned to the Triple-A Nashville Sounds.

On November 18, 2014, Molleken signed a minor league contract with the Cleveland Indians organization.

[7] After starting the season in Triple-A, on June 20, 2016, Molleken had his contract purchased and was added to the 25-man roster when journeyman Casey McGehee was designated for assignment.

On February 19, 2020, Molleken signed with the Tecolotes de los Dos Laredos of the Mexican League.