This study reports the mechanical response of distinct carbon nanotube (CNT) morphologies as revealed by flat punch in situ nanoindentation in a scanning electron microscope. We find that the location of incipient deformation varies significantly by changing the CNT growth parameters. The initial buckles formed close to the growth substrate in 70 and 190 μm tall CNT forests grown with low pressure chemical vapor deposition (LPCVD) and moved to 100 μm above the growth substrate when the height increased to 280 μm. Change of the recipe from LPCVD to CVD at pressures near atmospheric changed the location of the initial buckling event from the bottom half to the top half of the CNT forest. Plasma pretreatment of the catalyst also resulted in a unique CNT forest morphology in which deformation started by bending and buckling of the CNT tips. We find that the vertical gradients in CNT morphology dictate the location of incipient buckling. These new insights are critical in the design of CNT forests for a variety of applications where mechanical contact is important.