Materials and elements with a high melting point, including molybdenum, are suitable for high temperature physical applications and the fabrication of components such as welding electrodes or wires to be used in spark erosion wire-cut machines. The classic, or conventional, approaches to machining pure molybdenum are aptly complemented with the frequently used unconventional wire electrical discharge machining (WEDM) method. This paper proposes a detailed analysis of a WEDM-machined surface and its defects, as related to a welding electrode. Comprehensive information on the topography, including a 3D color-filtered representation of the surface, was acquired using a contact profiler and an atomic force microscope (AFM). The defects of the machined surfaces were examined with electron microscopy, both directly on the surface of a given sample and within its cross section. The entire set of associated processes also involved a local analysis of the chemical composition of the subsurface layer and a measurement of the relevant hardness.