The most commonly used models (based on the Method of Characteristics numerical scheme) for column separation in liquid pipes assume that the vapor pocket occupies the whole cross sectional area of the pipe. Beyond the right and the left boundaries of the vapor pocket the pipe cross sectional area is full of liquid. However, under certain conditions, depending on the pipe gradient, flow rate, etc., the piping downstream of the high elevation point may have flow that only occupies a portion of the pipe cross section. The empty region of the pipe will consist of vapor formed due to the flashing of the liquid. The conventional methodology used for the analysis of column separation cannot be applied under such conditions. A MOC based calculation scheme is developed, which treats the partially filled regions of the piping system as open channel flow. It is generalized to allow for transition from partially full to full flow conditions, and vice-versa. This methodology has been incorporated into the computer program HSTA (Hydraulic Systems Transient Analysis) and the advantages/limitations of the various methodologies are compared.