A method for forming contact holes using a multi-layer hard mask. A substrate with a device region and an alignment region having an opening therein to serve as an alignment mark is provided. A dielectric layer is formed overlying the substrate and fills the opening, followed by the multi-layer hard mask. The multi-layer hard mask over the opening is partially removed and that on the device region is patterned to form a plurality of holes therein and expose the underlying dielectric layer. The exposed dielectric layer on the device region is etched to form the plurality of contact holes therein.