We have investigated the impact of shrinking feature sizes on the sputter efficiency of focused ion beams on crystalline silicon. On the basis of this analysis, we have demonstrated the main competitive mechanisms determining the complex response of silicon. Low-dose irradiation with a 50-keV Ga⁺ beam in the range from 10¹³ ions/cm² to 10¹⁵ ions/cm² produced pronounced swelling of the silicon due to amorphization. Higher doses led to material removal with an efficiency of about 2.5 atoms/ion. A sputter yield promoting the self-focusing effect combined with the sputter rate increase at oblique angles, and an opposing dose-deficiency effect, determined the complex characteristics of nanoscale trench milling. Shrinking critical dimensions led to higher sputter yields, attributable to self-focusing effects of incident ions becoming dominant at aspect ratios in the region of unity. At aspect ratios beyond unity, re-deposition was the dominant effect.