The invention provides a system and process of patterning structures on a carbon based surface comprising exposing part of the surface to an ion flux, such that material properties of the exposed surface are modified to provide a hard mask effect on the surface. A further step of etching unexposed parts of the surface forms the structures on the surface. The inventors have discovered that by controlling the ion exposure, alteration of the surface structure at the top surface provides a mask pattern, without substantially removing any material from the exposed surface. The mask allows for subsequent ion etching of unexposed areas of the surface leaving the exposed areas raised relative to the unexposed areas thus manufacturing patterns onto the surface. For example, a Ga+ focussed ion beam exposes a pattern onto a diamond surface which produces such a pattern after its exposure to a plasma etch. The invention is particularly suitable for patterning of clear well-defined structures down to nano-scale dimensions.