Organic (bone, antler, wood) knapping tools were undoubtedly a component of early human tool kits since the Lower Palaeolithic. Previous studies have identified pitting and the occasional presence of embedded flint flakes as important features for recognizing archaeological bone and antler percussors. However, no systematic protocol of analysis has been suggested for the study of this rare archaeological material. Here we present qualitative and quantitative results of a preliminary analysis of an experimental knapping hammer, using a novel combination of microscopy (focus variation optical microscope and scanning electron microscope), micro-CT scanning and energy dispersive X-ray spectroscopy. These imaging and analytical techniques are used to characterize use-damage from the manufacture of handaxes. This paper highlights the strengths and weakness of each technique. Use-wear on the working area included attritional bone loss, micro-striations and compaction of the outer layer of the antler matrix from repeated hitting of the beam against the sharp edge of the handaxe during knapping. Embedded flint flakes were also identified in the pits and grooves. This combination of high-resolution imaging techniques is applicable to fragile archaeological specimens, including those encrusted by sediment or encased in matrix.