Combining the strengths of atomic layer deposition (ALD) with focused ion beam (FIB) milling provides new opportunities for making 3D nanostructures with flexible choice of materials. Such structures are of interest in prototyping microelectronic and MEMS devices which utilize ALD grown thin films. As-milled silicon structures suffer from segregation and roughening upon heating, however. ALD processes are typically performed at 200–500 °C, which makes thermal stability of the milled structures a critical issue. In this work Si substrates were milled with different gallium ion beam incident angles and then annealed at 250 °C. The amount of implanted gallium was found to rapidly decrease with increasing incident angle with respect of surface normal, which therefore improves the thermal stability of the milled features. 60° incident angle was found as the best compromise with respect to thermal stability and ease of milling. ALD Al2O3 growth at 250 °C on the gallium FIB milled silicon was possible in all cases, even when segregation was taking place. ALD Al2O3 could be used both for creating a chemically uniform surface and for controlled narrowing of FIB milled trenches.