A method is provided for forming a polysilicon layer on a substrate and aligning an exposure system with an alignment feature of the substrate through the polysilicon layer. In such method, a polysilicon layer is deposited over the substrate having the alignment feature such that the polysilicon layer reaches a first temperature. The polysilicon layer is then annealed with the substrate to raise the polysilicon layer to a second temperature higher than the first temperature. A photoimageable layer is then deposited over the polysilicon layer, after which an alignment signal including light from the alignment feature is received through the annealed polysilicon layer. Using the alignment signal passing through the annealed polysilicon layer from the alignment feature, an exposure system is aligned with the substrate with improved results.