A method for etching magnetic and ferroelectric materials using a pulsed substrate biasing technique (PSBT) that applies a plurality of processing cycles to the substrate, where each cycle comprises a period of plasma etching without substrate bias and a period of plasma etching with the substrate bias. In exemplary applications, the method is used for fabricating magneto-resistive random access memory (MRAM) and ferroelectric random access memory (FeRAM) devices.