This work investigates the critical issues in the focused ion beam (FIB) nanopatterning of semiconducting devices. Matrixes of holes with diameter of about 150 nm were drilled by FIB on the topmost layers of a quantum dot based device. In order to study the presence of artefacts in the active region of the device, the milling parameters were investigated. A careful analysis of the ion beam effects on the structural and morphological features of the holes, mainly due to the heterogeneous composition of the layers to be milled, demonstrated that important deviations from the expected structures, in terms of size, shape and geometry of the holes, as well as layer amorphization and damage, occur.