In this work we report on studies of the modification of a surface of gallium arsenide GaAs during irradiation by heavy cesium (Cs+) ions during secondary ion mass spectrometry (SIMS) measurements. The surface roughness was investigated by measuring the distribution of heights at the surface of the samples by atomic force microscopy (AFM), with their subsequent statistical processing. We observed both an increase, and a reduction of the integrated root-mean-square height (RMS) depending on the sample preparation. The analysis of the structural function has allowed us to estimate the characteristic lateral sizes of surface structures arising during ion sputtering. It was established, that in a lateral range of about 1–100 nm, the roughness of the surface of the gallium arsenide increases for all investigated samples.