We report on optimisation of the side wall angle of focused ion beam (FIB) fabricated submicron diameter holes in silicon. Two optimisation steps were performed. First, we compare two different FIB scanning procedures and show the advantages of using a spiral scanning method for the definition of holes in photonic crystal slab structures. Secondly, we investigate the effect on the geometry, of parameters for reducing the tapering effect. Furthermore, we report on the initial results regarding effects of Ga+ ion implantation during FIB milling on optical losses, both before and after an annealing step, showing over a decade reduction of optical loss