In this paper, we describe a modification of the classical hot embossing process which is capable of producing holes in polymer substrates. Substrates with holes that penetrate the complete height of the substrate have been a technical challenge since the first description of the hot embossing process. However most components as, e.g., microfluidic components targeted for biomedical applications are in need of such structures. We describe a simple and robust approach which enables the user to produce holes in polymer substrates without the need for elaborate machine equipment or special production technology for molding tools. We call this process hot punching which we demonstrate here to be suitable not only for small scale substrates but also for producing substrates with holes on an 8 inch substrate.