This paper describes a new technique for removing the background level from digital images produced in comprehensive two-dimensional gas chromatography (GCxGC). Background removal is an important first step in the larger problem of quantitative analysis. The approach estimates the background level across the chromatographic image based on structural and statistical properties of GCxGC data. Then, the background level is subtracted from the image, producing a chromatogram in which the peaks rise above a near-zero mean background. After the background level is removed, further analysis is required to determine the quantitative relationship between the peaks and chemicals in the sample. The algorithm is demonstrated experimentally to be effective at determining and removing the background level from GCxGC images. The algorithm has several parametric controls and is incorporated into an interactive program with graphical interface for rapid and accurate detection of GCxGC peaks.