Microhot-embossing is a less complex and inexpensive alternative over standard photolithography for patterning poly(lactic acid) (PLA) films. However, direct patterning of discrete or through-thickness microstructures by conventional microhot-embossing is not possible due to embossing-caused residual film. Use of complex modifications in the embossing process can further prohibit its integration with other standard semiconductor fabrication processes. Plasma-based reactive ion etching (RIE) of embossing-caused PLA residual film can be a viable option potentially allowing integration of the conventional hot-embossing process with standard semiconductor fabrication processes. RIE etch-rates of PLA packaging films, hot-embossed with parylene-based thin-film cochlear implant-shaped stiffener structures, were characterized for oxygen (O2), nitrogen (N2), and argon (Ar) plasmas under two different process conditions. The etch-rates of PLA films for O2, N2, and Ar plasmas were 0.29–0.72 μm/min, 0.09–0.14 μm/min, and 0.11–0.15 μm/min, respectively. Complete removal of embossing-caused residual film has been demonstrated utilizing the etching results for O2 plasma. Also, the effect of RIE etching on resultant PLA film surface roughness has been quantified for the three plasmas.