A trenched-substrate based lens manufacturing method includes depositing lens material on a first side of a substrate, wherein the first side of the substrate has a plurality of trenches. The method further includes shaping a plurality of lens elements from the lens material. The method includes shaping the plurality of lens elements, on a respective plurality of surface portions of the first side, by contacting a mold to the first side. Each of the surface portions are adjacent a respective one of the trenches. Additionally, the method includes accommodating an excess portion of the lens material in the trenches. A lens system, manufactured using this method, includes a substrate with a planar surface and a trench embedded in the planar surface. The lens system further includes a lens element molded on the planar surface adjacent to the trench.