This article shows the fabrication process and packaging of through polymer optical vias (TPOV). The TPOV enables encapsulation and packaging of silicon photonic systems using film assisted molding (FAM) and the creation of micron-sized through polymer optical vias. The optical vias are lithographically defined in thick film photo-resist (∼ 300 μm) and parallel processed on substrate level. Placing and connecting optical windows on individual chips using pick & place is a difficult and time-consuming process because of the stringent requirements on alignment accuracy, cost and throughput. In this work we provide a solution to this problem by combining microfabrication technology with back-end film assisted molding technology for a new packaging approach for the integration of optical windows. As feasibility study we show through polymer optical windows on optical encoder Si photodiode arrays. The resulting microstructures are transparent in the spectrum of interest and hence serve as optical windows towards the substrate. Furthermore, our results show that the high aspect ratio (5:1) micro structure windows can be achieved and protected using FAM-technology. The optical through package windows are accurately defined (±5 μm accuracy due to mask limitations) and can significantly improve the throughput. The total process time of a single wafer with up to 1260 chips and 20160 windows, including lamination, exposure and development, would approximately take 1-1.5 hours.