As advanced photolithography extends the ability to print feature sizes below the 100 nm technology node, various reticle enhancement techniques (RET) are being employed to improve resolution. An example of RET is the alternating phase shift mask (APSM), which currently challenges the ability of conventional repair techniques to repair even the most basic reticle defect. The phase shifting quartz bump is one defect type critical to the performance of APSM technology masks. These defects on the APSM reticle are caused by imperfections in the resist image during processing, resulting in a localized under or over etch of the quartz substrate. The integrated application of gas assisted etch (GAE), focused ion beam (FIB) reticle repair, and atomic force microscopy (AFM), provides a comprehensive solution for advanced reticle defect repair and characterization. Ion beam repair offers superior accuracy and precision for removal without significant damage to the underlying or adjacent quartz. The AFM technique provides quantitative measurement of 3D structures, including those associated with alternating phase shifters etched into quartz as well as embedded shifters. In the work presented in this paper, quartz bump defects were pre-scanned on an AFM tool and proprietary software algorithms were used to generate defect image and height map files for transfer to the FIB reticle repair tool via a network connection. The FIB tool then used these files to selectively control the ion dose during the corresponding quartz defect repair. A 193 nm APSM phase shift photomask with programmed defects in 400 nm line and space pattern was repaired using an FEI Stylus NanoProfilometer (SNP) and a FEI Accura 850 focus ion beam (FIB) tool. Using the APSM FIB repair method, the transmittance evaluated from 193 nm AIMS at the repair area was more than 90% without post-processing.