The technology node of semiconductor device production is progressing to 65nm generation. For the 65nm photomasks, the target specifications of defect size and repair accuracy are 52nm and 7nm, respectively. Especially, real defects on photomasks are not only simple two-dimensional patterns but also three-dimensional shapes such as phase shift defects and contamination, thus we need to recognize defect shapes accurately. Additionally, AAPSM's Cr patterns overhang, and we have to measure defects on three-dimensional shapes. To evaluate them, we use an AFM metrology system, Dimension X3D (Veeco), having both precise CD measurement repeatability (2nm) and high resolution for defects. In this report, we show the performance of the AFM metrology system. First, we evaluated CD metrology performance, CD repeatbility about four type photomasks: NEGA-BIM, POSI-BIM, KrF-HT and ArF-HT, and all masks met specifications. Next, we evaluated defect pattern shapes and AAPSM and CPL mask patterns. Consequently, we have confirmed that the AFM metrology system has high performance for 65nm photomasks.