In this work, we studied the effect of the pregrowth annealing temperature on the epitaxial growth of GaAs on modified Si area. It is shown that an increase in the annealing temperature leads to a decrease in the selectivity of GaAs epitaxial growth, as well as to a transition from two-dimensional like growth to the growth of nanowires. At an accelerating voltage of 10 kV, 5 passes of the focused ion beam, and an annealing temperature of 600 °C, no epitaxial growth was observed on the modified areas. An increase in the accelerating voltage of the focused ion beam to 20 kV led to the onset of the formation of GaAs nanostructures at low values of the number of passes. An increase in the annealing temperature to 800 °C with the subsequent growth of GaAs leads to the activation of parasitic growth outside the modification regions over the entire range of accelerating voltages and the number of processing passes of the focused ion beam.