@ amihomo,
CST works on FDTD (Finite Difference Time Domain) and its also a differential equation approach. IE3D works on Integral equation based MoM.
Can you please explain your comment now for not using Radiation boundary condition in here.
@ Leon_80
I must say, as per the figures you uploaded with PEC and PMC boundary conditions, these are actually used to simulate the unit cell of metamaterials. I hope this is a filter that you intend to design. I can not say exactly but there is a pdf from HFSS on simulation of metamaterials where they have slightly mentioned the same structure as of yours.