Provided is an aligning method capable of setting a sample observation unit such as an optical microscope to a probe microscope observation position at high precision. A sample having a known structure is used in advance. A surface of the sample and a shape of a cantilever provided with a probe are observed using the sample observation unit such as the optical microscope. A sample observation position and a probe position which are obtained using the sample observation unit are verified, and a relative positional relationship therebetween is recorded. Then, a first mark indicating a position of the cantilever and a second mark which is displayed in conjunction with the first mark and has the relative positional relationship with the first mark are produced to align the sample relative to the second mark.