We have investigated the efficiency of bifunctional pattern formation in alkanethiolate self-assembled monolayers (SAMs) adsorbed on GaAs (001) and Au, using time-of-flight secondary ion mass spectrometry. Two patterning techniques were employed: electron beam lithography and UV photopatterning. Previous work has always assumed that complete degradation of the SAM was necessary for the Formation of well-defined multi functional patterned surfaces, requiring large electron doses or long UV irradiation times. We demonstrate that well-defined Multifunctional patterned surfaces can be produced on GaAs (001) with only partial degradation of the SAM, allowing greatly reduced electron beam doses and UV irradiation times to be used. Using electron beam lithography we observe that sharp well-defined patterns can form after an electron dose as low as 450 mu C cm(-2). We also demonstrate that only 50% of the monolayer must be photooxidized in UV photopatterning, reducing the exposure time needed by a factor of 3. In contrast, patterning of alkanethiolate SAMs adsorbed on Au requires much higher electron doses (>= 1250 mu C cm(-2)) and photooxidation times (2 h). The substantial differences observed on these two substrates appear to arise from differences in the SAM Structure on GaAs and Au. These results suggest that alkanethiolate SAM resists may be a suitable technology for nanometer scale lithography of GaAs and possibly other semiconductors.