Computer Aided Design (CAD) alignment is a key requirement for dynamic fault isolation. CAD alignment between the drawn layout and the physical reflected image from the device helps to navigate and observe the physical location of the suspected circuitry. Conventionally, large structures such as the boundaries of Static Random-Access Memory (SRAM) cells are used as reference for coarse CAD alignment and the shallow trench isolation (STI) layer is used for fine alignment while analyzing logic cell structures. With technology scaling, especially into FinFETs, the fine alignment has become more challenging as the reflected optical image of STI layer is poorly resolved. In this paper, we discuss the enhanced CAD alignment techniques in Synopsys Avalon that uses features “Minimum object size (dimension based)”, and “net search” developed in the CAD tool, Synopsys Avalon, combined with Amplitude lock-in Dynamic Photon Emission Microscopy (D-PEM) technique to assist a finer CAD alignment.