An analytical transmission and electron microscope study of diamond structures created using a Focused Ion Beam Hard Mask (FIBHM) technique is presented. From our findings we propose a novel hard mask mechanism for the patterning diamond which represents a new form of ion beam lithography. It involves a surface modification induced by a FIB implantation which, on exposure to a plasma etch, leads to the formation of a non-volatile platform on which components in the plasma can deposit to subsequently protect the underlying or unmasked material from etching in the same plasma environment. We show this mechanism describes the formation of diamond nano-whiskers being used for field emitters and biosensors. We also predict that it is effective for patterning silicon and explains similar masking behavior observed in the literature.