Example embodiments relate to methods and apparatuses for aligning a probe for scanning probe microscopy (SPM) to the tip of a pointed sample. One embodiments includes a method for aligning an SPM probe to an apex area of a free-standing tip of a pointed sample. The method includes providing an SPM apparatus that includes the SPM probe; a sample holder; a drive mechanism; and detection, control, and representation tools for acquiring and representing an image of a surface scanned by the SPM probe. The method also includes mounting the sample on the sample holder. Further, the method includes positioning the probe tip of the SPM, determining a 2-dimensional area that includes the pointed sample, performing an SPM acquisition scan, evaluating and acquired image, and placing the SPM probe in a position where it is aligned with an apex area of the free-standing tip of the pointed sample.