In this paper, we report on a theoretical framework based on Gaussian Beam Mode Analysis for modelling standing waves in submillimetre optical systems. Standing waves or multiple reflections have been traditionally difficult to model but this analytical method proves to be very versatile in first order predictions. In previous papers we reported on the underlining theory and described some important examples including reflections between a feed horn and telescope secondary mirror and also reflections between two coupled corrugated horns. This technique can in addition be applied to reflections between components such as lenses and apertures , . As our method uses a full multi-moded scattering matrix description of the feed horn (typically a corrugated horn), which is then transformed to equivalent free space Gaussian modes, multiple reflections between the source/detector device, located at the back of the horn, and any arbitrary surface in the optical path can be accurately analysed. An in-depth overview of the technique is presented including analysis of the eigenmodes or most natural mode set that describes the standing wave itself that can exist within a quasioptical system, which we hope will give new insights into optical cavity phenomena. We investigate mechanisms to reduce standing wave ripples often present in submillimeter optics and try to understand more deeply the form and structure of the reflected power component.