We report the structural modifications of vertically grown carbon nanotubes (VCNT) by plasma ion bombardments. The VCNT were grown by thermal chemical vapor deposition (CVD) using acetylene feedstock with iron catalyst and alumina supporting layers on silicon substrate. The plasma ion bombardments were performed using DC plasma enhanced CVD with parallel electrodes configuration. As a result, the height of the as-grown VCNT decreased with increasing applied bias voltages, plasma powers and working pressures. In addition, we observed the aggregated morphologies of the VCNT top surface after the plasma treatments which would be useful for field emission display and energy storage applications.