The micropatterning of layers of colloidal quantum dots (QDs) stabilized by inorganic ligands is demonstrated using PbS core and CdSe/CdS core/shell QDs. A layer-by-layer approach is used to assemble the QD films, where each cycle involves the deposition of a QD layer by dipcoating, and the replacement of the native organic ligands by inorganic moieties, such as OH- and S2-, followed by a thorough cleaning of the resulting film. This results in a smooth and crack-free QD film on which a photoresist can be spun. The micropatterns are defined by a positive photoresist, followed by the removal of uncovered QDs by selective wet etching with an HCl/H3PO4 mixture. The resulting patterns can have submicron feature dimensions, limited by the resolution of the lithographic process, and can be formed on planar and 3D substrates. It is shown that the photolithography and wet etching steps have little effect on the photoluminescence quantum yield of CdSe/CdS QDs. Compared with the unpatterned CdSe/CdS QD film, only a 10% degradation in the quantum yield is observed. These results demonstrate the feasibility of the proposed micropatterning method to implement the large-scale device integration of colloidal quantum dots.