Mask defect repair is a key part of manufacturing high quality masks. Issues such as low-level transmission defect have not been solved. A series of experiments was conducted to review the effects of gallium staining generated by older generation (FIB) focused ion beam repair tool. Deposition and chemical etching with a FIB tool is done in order to correct the defective areas. Dispersion of chemicals in a molecular beam to the area of interest with a well-defined amount of molecules and monolayers will ensure correct amount of material is removed. This repair technique-using FIB, results in other problems that impacts light transmission. This effect of transmission becomes an issue at extremes of focus exposure matrix. Gallium implantation defect resulting from focusing gallium ion beams to repair is not a killer Deep UV (DUV) defect since it is considered to be an invisible transmission type. We will discuss how an attempt to repair chrome extension defect on contact-hole mask lead to edge placement problems. This is due to defects can be invisible to blue lasers in mask inspection systems, and can still be printed on wafer. A detailed study on how to characterize these problems using different methods and tools will be discussed.