Methods and systems for watermarking a circuit design include defining a watermarked cell library that includes cells, each of which defines a design structure that corresponds to a manufacturable physical structure, at least one of which being a watermarked call that includes a watermark. The watermark is encoded using a design structure that extends beyond a respective cell boundary. A first circuit design file is generated for a device to be manufactured. The first circuit design file including at least one watermarked cell. The first circuit design file is sent to a manufacturer for fabrication of a corresponding device that includes a watermark structure that encodes an identifier.