The packaging of a microchip affects its size, performance and cost. With advanced packaging, more efficient and smaller microchips can be produced. For this, advanced packaging stepper systems are used, which are lithography machines with a highly optimized projection lens system, that use a powerful light source. The projection lens system for lithography machines are highly accurate optical assemblies with stringent optical requirements, such as a small wavefront error. These requirements need to be fulfilled, while also dealing with a high throughput. Due to the high throughput and the powerful light source, some of the light passing the projection lens system gets absorbed by the lenses. This causes local lens heating, which degrades the optical performance. Local lens heating causes thermal gradients to arise in the lenses, which cause refractive index gradients. Due to thermal expansion, the lenses will also deform, therefore changing the geometry of the optical surfaces. To analyze the lens heating effects, a Structural, Thermal and Optical Performance (STOP) analysis is performed. A multiphysics Finite Element Method (FEM) analysis model is build in COMSOL, which couples the structural, thermal and optical physics in a single model, which can model both steady-state and transient behaviour.