A scanning probe inspector comprises: a probe that includes a cantilever and a tip whose length corresponds to a depth of a trench that is formed in a wafer; a trench detector that acquires location information of the trench using the probe, where the location information includes depth information of the trench; a controller that inserts the tip into a first point where there exists a trench based on the location information of the trench, and moves the tip through the trench using the location information of the trench; and a defect detector that detects a presence of a defect in a sidewall of the trench as the tip is moved through the trench.