Second-generation self-assembling bis-urea macrocycles were designed that form columnar structures in the solid state. The new macrocycles were constructed from more flexible building blocks yielding greater solubility and a more efficient synthesis. In addition, heteroatoms in the form of ether oxygens were incorporated in the walls of the macrocycles to provide additional recognition sites for guest encapsulation. We observed reduced fidelity of the stacking motif and in some cases the intermolecular urea-urea hydrogen bonds were disrupted by the formation of intramolecular hydrogen bonds. We also observed new offset assembly motifs that maintained the urea-urea interaction. These results suggest that the stacking of the arene units in the rigid first-generation systems was an important factor in guiding the formation of the columnar stacks.