Diminshing feature size, combined with requirements for higher throughput during quality control, have steadily increased demand for Critical Dimension Atomic Force Microscopy (CD AFM). In contrast to Scanning Electron Microscopy (SEM), the CD AFM provides a solution for nondestructive and rapid 3-dimensional measurementof features with 1.5nm 3s repeatability at the 65nm node size. Specifically for these stringent AFM measurements, it is critical to both remove the effects of the complex probe shape on the acquired image, and to dynamically monitor the condition of the probes used during scanning via in-situ caliberation.