Microstructuring techniques, such as laser direct writing, enable the integration of microstructures into conventional polymer lens systems and may be used to generate advanced functionality. Hybrid polymer lenses combining multiple functions such as diffraction and refraction in a single component become possible. In this paper, a process chain to enable encapsulated and aligned optical systems with advanced functionality in a cost-efficient way is presented. Within a surface diameter of 30 mm, diffractive optical microstructures are integrated in an optical system based on two conventional polymer lenses. To ensure precise alignment between the lens surfaces and the microstructure, resist-coated ultra-precision-turned brass substrates are structured via laser direct writing, and the resulting master structures with a height of less than 0.002 mm are replicated into metallic nickel plates via electroforming. The functionality of the lens system is demonstrated through the production of a zero refractive element. This approach provides a cost-efficient and highly accurate method for producing complicated optical systems with integrated alignment and advanced functionality.