An apparatus and method are provided for processing the images obtained from an atomic force microscopy when profiling high aspect ratio features. A deconvolution technique for deconvolving the sample image includes the use of multiple images but does not require exact calibration of the scanning probe. In one embodiment, erosion and dilation techniques are used to obtain an undistorted image of the sample being measured. In another embodiment, Legendre transforms are used to obtain an undistorted image of the sample being measured. Also described is a technique for measuring the tip radius of the scanning probe.