Possibility to form three-dimensional (3D) micro-structures in silicone elastomer (polydimethylsiloxane; PDMS) doped with different photo-initiators was systematically investigated using direct laser writing with femtosecond laser pulses at different exposure conditions. Accuracy of the 3D structuring with resolution of ~5 μm and a fabrication throughput of ~720 μm(3)/s, which is exceeding the previously reported values by ~ 300(×), was achieved. Practical recording velocities of ~ 1 mm/s were used in PDMS with isopropyl-9H-thioxanthen-9-one (ISO) and thioxanthen-9-one (THIO) photo-initiators which both have absorption at around 360 nm wavelength. The 3D laser fabrication in PDMS without any photo-initiator resulting in a fully bio-compatible material has been achieved for the first time. Rates of multi-photon absorption and avalanche for the structuring of silicone are revealed: the two-photon absorption is seeding the avalanche of a radical generation for subsequent cross-linking. Direct writing enables a maskless manufacturing of molds for soft-lithography and 3D components for microfluidics as well as scaffolds for grafts in biomedical applications.