The modeling of millimeter and sub-millimeter-wave optical systems requires special approaches. In many systems the beams can be considered to be coherent and their propagation can be efficiently modeled using modal analysis, especially useful for quick design purposes. Physical optics is also a useful tool when detailed analysis is required. Modal analysis in general, however, is a very powerful technique, which enables one also to understand issues associated with throughput when partially coherent systems and arrays are being considered. In the paper we discuss these issues and present some examples from millimeter and submillimeter wave astronomical instrumentation.