Method of encapsulating a semiconductor structure comprising providing a semiconductor structure comprising an opto-electric element located in a cavity formed between a substrate and a cap layer, the cap layer being made of a material transparent to light, and having a flat upper surface; forming at least one protrusion on the cap layer; bringing the at least one protrusion of the cap layer in contact with a tool having a flat surface region, and applying a opaque material to the semiconductor structure where it is not in contact with the tool; and removing the tool thereby providing an encapsulated optical semiconductor device having a transparent window integrally formed with the cap layer.