A new technique for micropatterning Fe-based bulk metallic glass surfaces is reported. The transpassive dissolution process is utilized for a defined localized material removal when using a pulsed electrochemical micromachining process. By applying submicrosecond pulses between a work piece and a tool electrode, microholes of high aspect ratio and depth of up to 100 μm can be machined into the bulk glassy Fe65.5Cr4Mo4Ga4P12C5B5.5 alloy. Two potential electrolytes are identified for the machining process. For these electrolytes, different reaction mechanisms are discussed. The possibility of machining more complex structures is demonstrated for the most promising electrolyte, a methanolic H2SO4solution. The impact of the process parameters, pulse length and pulse voltage, on the machining gap and the surface quality of the machined structures is evaluated.