Optoelectronic modules include an optoelectronic device and a transparent cover. A non-transparent material is provided on the sidewalls of the transparent cover, which can help reduce light leakage from the sides of the transparent cover or can help reduce stray light from entering the module. The modules can be fabricated, for example, in wafer-level processes. In some implementations, openings such as trenches are formed in a transparent wafer. The trenches then can be filled with a non-transparent material using, for example, a vacuum injection tool. When a wafer-stack including the trench-filled transparent wafer subsequently is separated into individual modules, the result is that each module can include a transparent cover having sidewalls that are covered by the non-transparent material.