One critical area for EUV lithography is the development of appropriate mask repair strategies. To this end, we have explored etching repair strategies for nickel absorber layers and focused electron beam induced deposition of ruthenium capping layers. Nickel has higher EUV absorption than the standard TaN absorber layer and thus thinner films and improved optical quality can be realized. A thin (2.5 nm) ruthenium film is commonly used as a protective capping layer on the Mo-Si EUV multi-layer mirror which mechanically and chemically protects the multi-layers during standard mask-making procedures. The gas field ion (GFIS) microscope was used to investigate helium and neon ion beam induced etching (IBIE) of nickel as a candidate technique for EUV lithography mask editing. No discernable nickel etching was observed for helium, however transmission electron microscopy (TEM) revealed subsurface damage to the underlying Mo-Si multilayers. Subsequently, neon beam induced etching at 30 keV was investigated and successfully removed the 50 nm nickel absorber film. TEM imaging also revealed subsurface damage in the underlying Mo-Si multilayer. Two damage regimes were apparent, namely: 1) beam induced mixing of the Mo-Si layers and 2) nanobubble formation. Monte Carlo simulations were performed and the observed damage regimes were correlated to: 1) the nuclear energy loss and 2) a critical implant concentration. Electron beam induced deposition (EBID) was explored to deposit ruthenium capping/protective layers. Several ruthenium precursors were screened and so far liquid bis(ethylcyclopentyldienyl)ruthenium(II) was successful. The purity of the as-deposited nanodeposits was estimated to be 10% Ru and 90% C. We demonstrate a new chemically assisted electron beam purification process to remove carbon by-products and show that high-fidelity nanoscale ruthenium repairs can be realized.