Microholes for the production of gasoline direct injection nozzles were obtained by ultrashort pulsed laser machining in martensitic stainless steels. The inner surface analysis was carried out by a specifically conceived Scanning Probe Microscopy instrument and revealed the presence of periodic surface microstructures whose formation was studied as a function of process parameters (pulse energy, repetition rate, rotational speed, drilling strategy). Experiments demonstrated that geometrical features of the microstructures can be varied by a proper parameter selection and open the perspective for an optimized process enabling a reduction of coking accumulation during service life and a more effective atomization of the fuel jet.