Silicon is an excellent material for microelectronics and integrated photonics with untapped potential for mid-IR optics. Despite broad recognition of the importance of the third dimension, current lithography methods do not allow fabrication of photonic devices and functional microelements directly inside silicon chips. Even relatively simple curved geometries cannot be realized with techniques like reactive ion etching. Embedded optical elements, like in glass, electronic devices and better electronic-photonic integration are lacking. Here, we demonstrate laser-based fabrication of complex 3D structures deep inside silicon using 1 micrometer-sized dots and rod-like structures of adjustable length as basic building blocks. The laser-modified Si has a different optical index than unmodified parts, which enables numerous photonic devices. Optionally, these parts are chemically etched to produce desired 3D shapes. We exemplify a plethora of subsurface, i.e., in-chip microstructures for microfluidic cooling of chips, vias, MEMS, photovoltaic applications and photonic devices that match or surpass the corresponding state-of-the-art device performances.