In this work, the effects of the focus ion beam (FIB) milling process on the optical properties of semiconductor nanostructures were investigated. With this aim, a sensitive materials system based on InGaAs/GaAs quantum dots with well known and excellent optical properties was selected for the FIB treatment. The FIB technique was used to locally remove a metallic mask deposited on top of the quantum dot sample. The photoluminescence (PL) signal, collected from the circular openings, was used to infer the possible damage effects of the ion beam on the properties of the dots.