When fabricating nanowires (NWs) in a doubly-clamped beam configuration it is possible for a residual axial stress to be generated. Here, we show that material characterisation of metal and semiconductor NWs subjected to residual axial stress can be problematic. Benchmark measurements of the Young's modulus of NWs are performed by sectioning a doubly-clamped NW into two cantilevered wires, eliminating residual axial stress. Use of models for doubly-clamped beams that incorporate the effects of residual stress are found to lead to ambiguity in the extracted Young's modulus as a function of displacement fit range, even for NWs with no residual stress. This is due to coupling of bending and axial stress effects at small displacements, and the limited displacement range of force curves prior to fracture or plastic deformation. This study highlights the importance of fabricating metal and semiconductor NWs that exhibit little or no residual axial stress for materials characterisation.