In this study, the generation of 3D microstructures in stainless steel with ultrashort laser pulses using different burst modes will be presented. Femtosecond laser pulses in the BiBurst mode and picosecond laser pulses in the MHz burst mode are used to generate a predefined 3D microstructure. To smooth the structure bottoms and to remove deposits, a novel subsequent processing technique using femtosecond laser pulses in the GHz burst mode is performed. Two different processing strategies of the ablation and the subsequent treatment are applied to generate predefined 3D microstructures with low surface roughness and without deposits. In this way, smooth structure bottoms with a minimum surface roughness of 0.13μm can be obtained at a structure depth of 300μm.