In current scanning-probe nanolithography research substrates consisting of octadecyl trichlorosilane monolayers on silicon are often used. On one hand, the presence of an organic monolayer can be used passive resist, influencing the formation of silicon dioxide on the substrate, whereas in other cases the monolayer itself is patterned, creating local chemical functionality. In this study we investigate the time scales involved in either process. By looking at friction and height images of lines oxidized at different bias voltages and different pulse durations, we have determined the parameter space in which the formation of silicon dioxide is dominant as well as the region in which the oxidation of the monolayer itself is dominant.