There are low target-to-background contrast, blurred edge and stronger noise in the infrared images which are always used in precise guidance. When applied to process the images, the traditional methods cannot get better processing result, because it cannot compress the noise effectively. But the soft mathematical morphological filter is non-linear filter and has many merits such as less sensitivity, higher computation speed etc. So it is well adapted to infrared images processing. The main performance of the soft morphological filter depends on different morphological exchange types and structuring elements. Unfortunately, there are no analytical criteria for choosing these structuring parameters. In order to obtain better image processing result, we must choose the most suitable structuring system based on specific task of image processing. In this paper, we take advantage of the profile and IR properties of ship to determine the shape and size of the structuring elements, and use the threshold theory to determine the values of structuring elements. The structuring system is applied to actual IR ship images. Some processing results are also listed in this paper. After the comparing of different results, a suitable structuring system is given at last.