A focused ion beam has been used to mill both individual carbon fibres as well as fibres in an epoxy composite, with a view to preparing flat surfaces for nano-indentation. The milled surfaces have been assessed for damage using scanning probe microscopy nano-indentation and Raman micro-probe analysis, revealing that FIB milling damages the carbon fibre surface and covers surrounding areas with debris of disordered carbon. The debris is detected as far as 100 gm from the milling site. The energy of milling as well as the orientation of the beam was varied and shown to have an effect when assessed by Raman spectroscopy. Crown Copyright (C) 2015 Published by Elsevier B.V. All rights reserved.