A method for forming contact holes using a partially recessed hard mask. A substrate with a device region and an alignment region having an opening therein, acting as an alignment mark, is provided. A dielectric layer is formed overlying the substrate and fills the opening. A polysilicon layer is formed on the dielectric layer, with over the opening on the alignment region comprising a recessed region and on the device region comprising a plurality of holes therein to expose the underlying dielectric layer. The exposed dielectric layer on the device region is etched to form contact holes therein.