The critical dimension (CD) specification of photomask for semiconductor integrated circuit patterning at a 90nm node and below is becoming unprecedentedly stringent. To meet the tight ITRS roadmap requirement, reticle makers have to rely heavily on advanced dimension metrology to characterize and control the processes of novel materials, new structures, and shrinking mask enhancement features. This paper evaluates a new generation of atomic force microscopy (AFM) for imaging and measuring the full three-dimensional (3D) shape of features. Cross-section sidewall profile, linewidth, and depth of etched mask features are evaluated at different steps of the mask making process. The impact of AFM probe characterization on the metrology capability to achieve nanoscale precision and accuracy is quantified. Tip shape parameters and tip wear are evaluated for a variety of mask materials for depth, linewidth, and sidewall profile measurements. The scanning probe based technique provides an absolute and direct measure of mask features anywhere within a plate, regardless of the material characteristics. Representative results on linewidth (for CD control), depth (for phase shift control), and sidewall profile (etch profile control) of etched masks are presented. The CD AFM data can help engineers better characterize and analyze the process and improve process control for mask development and manufacturing.