Self-assembled monolayers of octadecylthiol on GaAs and octadecylsiloxanes on titanium, aluminum, and silicon have been used as electron beam resists for plasma etching into the substrates. An electron cyclotron resonance source was used to excite a low-pressure, high-density plasma with low ion energy to achieve high selectivity with the thin masking layers. Patterning of monolayers on GaAs usually produced a negative tone, but etching of the metal surfaces resulted in positive tone patterning. The maximum etch depth into the GaAs was similar to 100 nm using the negative tone process. Lines have been etched into Ti with linewidths down to similar to 20 nm. The negative tone process can be explained by the cross linking of the monolayer under high-dose electron beam exposure; however, the positive tone process must rely on contrast either from different etching characteristics of the oxides or different structural arrangements of the different SAMs.