The invention is directed to methods for direct patterning of silicon. The invention provides the ability to fabricate complex surfaces in silicon with three dimensional features of high resolution and complex detail. The invention is suitable, for example, for use in soft lithography as embodiments of the invention can quickly create a master for use in soft lithography. In an embodiment of the invention, electrochemical etching of silicon, such as a silicon wafer, for example, is conducted while at least a portion of the silicon surface is exposed to an optical pattern. The etching creates porous silicon in the substrate, and removal of the porous silicon layer leaves a three-dimensional structure correlating to the optical pattern.