An inkjet printer is configured to capture image data of a bare rotating imaging surface and use the image data of the bare rotating imaging surface to remove noise from subsequent images of printed ink on the rotating imaging surface. A controller in the printer is configured to measure cross-correlations between margins in the bare rotating imaging surface image data and margins in the subsequent images of printed ink to identify areas of alignment between the image data of the bare rotating imaging surface and the subsequent images of printed ink. The data in the areas in the image data of the bare rotating imaging surface that are aligned with areas in the subsequent images are used to remove the background noise produced by structure in the rotating imaging surface.