The patterning and modification of organosilane self‐assembled monolayers on Si native oxide surfaces by low‐ and high‐energy ion beams were investigated. The nature and extent of low‐energy (50–140 eV) Ar+ion‐induced modification of a 2‐(trimethoxysilyl) ethyl‐2‐pyridine monolayer was studied by x‐ray photoelectron spectroscopy and by the quality of the electroless Ni patterns obtained. C(1s) and N(1s) core level x‐ray photoelectron spectroscopy indicated that the ion‐induced modification of the monolayer involved loss of the ethylpyridyl chain by sputtering and/or decomposition. The type of modification was independent of the ion energy and fluence, but the extent of modification depended on both parameters. The modification of the pyridine monolayer was monitored by the percent loss in the N(1s) peak area; modification commenced at a fluence of 5×1014ions/cm2and was observed for all ion energies studied. However, selective electroless metallization occurred only for monolayers that suffered ≳50% loss in the N(1s) x‐ray photoelectron spectroscopy signal. A damage saturation level of 80% N(1s) loss was indicated at an ion fluence of 9×1015ions/cm2. A high‐energy focused ion beam lithography system was also used to evaluate the high resolution patterning ofN‐(2‐aminoethyl)‐3‐aminopropyltrimethoxysilane, (aminoethylaminomethyl) phenethyltrimethoxysilane, and pyridine monolayers by Ga+, Si++, Au+, and Au++ions at energies ranging from 50 to 280 keV. The highest resolution metal features obtained were 0.3‐μm‐wide gaps on phenethyltrimethoxysilane and pyridine monolayers using Ga+and Si++ions. Aminopropyltrimethoxysilane monolayers were found to require ten times higher ion fluences to achieve comparable results with the phenethyltrimethoxysilane and pyridine monolayers for all ions investigated.