The self-assembly of colloidal crystals is important to the production of materials with functional optical, mechanical and conductive properties. Yet, self-assembly methods are limited by their slow kinetics and lack of structural control in space and time. Refinements such as templating and directed assembly partially address the problem, albeit by introducing fixed surface features such as templates or electrodes. A template-free method to reconfigure colloidal crystals simultaneously in three-dimensional space and time would better align work in colloidal assembly with materials applications. Here, we report a photo-induced assembly method that yields regions either filled with colloidal crystals or completely devoid of colloids. The origin of the effect is found to be electrophoresis of colloids generated by photochemistry at an indium tin oxide-coated substrate. Simple optical manipulations are applied to reconfigure these assembly and depletion regions. Thus, the method represents a new kind of template-free, reconfigurable three-dimensional photolithography.