A method for processing CT colonography input image voxel data representative of 3-dimensional images of a colon having gas and stool tagged with stool tagging agent, to remove the stool from the images. The input image voxel data is generated by an imaging instrument having a characteristic point spread function representative of instrument blurring. The point spread function of the instrument can be empirically determined, and the image data processed as a function of the point spread function to accurately identify and remove the tagged stool. In one embodiment of the invention, portions of the image data representative of the tagged stool and colon tissue are dilated as a function of the point spread function. In another embodiment, portions of the image data representative of the tagged stool are convolved with the point spread function to determine the fractional amount of stool present in the image portions, and the tagged stool subtracted by reducing the intensities of the associated portions of the image by an amount proportional to the fractional amount of stool present.