In this paper, an effective filter structure for filtering of target glint in tracking radar systems is used to improve the performance of CLOS(Command to Line-Of-Sight) guidance. The filter decouples range and angel channels to that it has a sound mathematical basis as well as computation efficiency as applied to the IMM algorithm. The effective filter structure in conjunction with CLOS guidance is tested by a series of simulation runs and it is shown to have superior performance compared with the other filter structures.