Helical structures play a vital role in nature, offering mechanical rigidity, chirality and structural definition to biological systems. Little is known about the influence of the helical architecture on the intrinsic properties of polymers. Here, we offer an insight into the nano architecture of helical polymers by measuring helical polyisocyanopeptides with single molecule force spectroscopy. An unprecedented large heterogeneity in the stiffness of the polymers was found. The heterogeneity persisted when the stiffness of these polymers was steered by: (1) enhancing the formation of the hydrogen bonding network along the polymer, (2) via pi-pi stacking interactions of aromatic perylenes, and (3) by changing the stereochemistry of the side chain. However, the heterogeneity was lost after completely disrupting the secondary structure by the addition of trifluoroacetic acid. Molecular dynamics simulations revealed three possible structural conformations which can account for the observed heterogeneity and their corresponding energy landscape is proposed.