© The Royal Society of Chemistry. Structure control such as diameter changes along single-walled carbon nanotubes (SWNTs) can be achieved in arrays of vertically aligned (VA-) SWNTs by switching the feedstock during growth. The local nature of the macroscopic transition from one diameter to another is then questioned as one can either envisage seamless transitions or discontinuous individual SWNTs. Here, we demonstrate that encapsulated molecules can serve as markers to doubtlessly identify seamless interconnections in macroscopic samples. A migration of nitrogen molecules inside the continuous SWNTs is observed using bulk scale measurements on double-layered SWNT arrays synthesized from different carbon/nitrogen feedstocks. The existence of N 2 molecules at the top of the SWNT arrays proves that there are continuous SWNTs throughout the double layered arrays with different diameters.