Conventional ion beam analysis (IBA) of deposited layers from fusion devices may have insufficient accuracy due to strongly uneven appearance of the layers. Surface roughness and spatial variation of the matrix composition make interpretation of broad beam spectra complex and non obvious. We discuss complications of applied IBA arising for fusion-relevant surfaces and demonstrate how quantification can be improved by employing micro IBA methods. The analysis is bound to pre-defined regions on the sample surface and can be extended by employing beams of several types, scanning electron microscopy (SEM) and stereo SEM techniques. (C) 2014 Elsevier B.V. All rights reserved.