To use atomic force microscope to measure narrow vertical features is challenging. Using carbon nanotube (CNT) probes is a possible remedy. However, even with its extremely high stiffness, van der Waals attractive force from steep sidewalls bends CNT probes. This probe deflection effect causes deformation (or “swelling”) of the measured profile. When measuring 100-nm-high vertical sidewalls with a 27-nm-diameter and 265-nm-long CNT probe, the probe deflection at the bottom is estimated as large as 5.8 nm. This phenomenon is inevitable when using long and thin probes. We proposed a method to correct this probe deflection effect. Detecting torsional motion of the base cantilever of the CNT probe makes it possible to estimate the CNT probe deflection. Using this information, we have developed a technique for correcting the probe deformation effect from measured profiles. This technique, in combination with correction of the probe shape effect, enables vertical sidewall profile measurement with AFM.