Wire electrical discharge machining is an unconventional machining technology that is crucial in many industries. The surface quality of the machined parts is carefully monitored, but the condition of the subsurface layer also plays a crucial role, especially in case of defects occurrence such as cracks or burnt cavities. The subsurface layer of individual materials is affected differently due to wire electrical discharge machining. For this reason, this study was carried out focusing on a detailed analysis of transmission electron microscope (TEM) lamella made of Ti-6Al-4V titanium alloy, AlZn6Mg2Cu aluminum alloy, pure molybdenum, Creusabro 4800 steel, and Hardox 400 steel. The attention was first of all paid to the concentration and distribution of individual elements in the recast layer and also in the base material, which was often affected by wire electrical discharge machining. Further, a diffraction analysis was performed for each TEM lamella in the adhesive area and in the base material area. In order to assess the macro-effects on the machined material, the topography analysis of the machined surfaces and the morphology analysis were performed using electron microscopy.