This paper presents DEM modeling of the setting of particles in liquids under conditions similar to sedimentation/filtration process. The liquid flow is supposed to be one-dimensional, and the motion of particles is three-dimensional. Various forces are incorporated in determining the motion of the particles, including the particle-particle interaction forces due to collision and the van der Waals attraction, and the particle-fluid interactions such as buoyancy, drag and lift forces. The model is validated by comparing the simulation and experiment results. The packing structures are analyzed in terms of porosity, radial distribution function and coordination number. The effects of key variables such as particle size, Hamaker constant, fluid density and viscosity are examined through a series of controlled numerical experiments. The roles of various forces related to these variables are also discussed.