You can't model a square/rectangular cross section with a pipe. This is because you can't get both the area and cross sectional inertia correct. In addition, the stress wouldn't be computed correctly because CAESAR II assumes all cross sections are circular. If the whole system is square/rectangular duct, you're better off using some other software package.

However, if you have just a short section, and most of the system is pipe, you can use the Structural Modeler to build user defined cross sections and then include these into your piping model. Naturally, stresses won't be computed on these user defined sections, but at least the analysis will be correct. You will obtain accurate displacements, element forces, and restraint loads with this method.