The porous properties of self-assembled waveguides made up of nanoparticles are characterised. Atomic force microscopy (AFM) reveals predominantly hcp or fcc packing suggesting a remarkably well ordered and distributed porous structure. N2 adsorption studies estimate a surface area SA ~ 101 m2/g, a total interstitial volume Vi ~ 1.7 mL/g and a pore size distribution of r ~ (2 - 6) nm. This distribution is in excellent agreement with the idealised values for identically sized particles obtained for the octahedral and tetrahedral pores of the hcp and fcc lattices, estimated to lie within and rtet ~ (2.2 – 3.3) nm and roct ~ (4.2 – 6.2) nm for particles varying in size over 20 to 30 nm. Optical transmission based percolation studies reveal rapid penetration of Rhodamine dye (< 5 s) with very little percolation of larger molecules such as ZnTPP observed under similar loading conditions. In the latter case, laser ablation was used to determine the transport of hydrated Zn2+ to be D ~ 3 x 10-4 nm2s-1. By comparison, ZnTPP was not able to percolate into the wire over the time of exposure, t = 10 mins, effectively demonstrating the self-assembled structure acting as a molecular sieve. We discuss the potential of such structures more broadly and conclude that the controllable distribution of such nano-chambers offers the possibility of amplifying, or up-scaling, an otherwise local interaction or nanoreactions to make detection and diagnostics much simpler; it also opens up a new approach to material engineering making new composites with periodic nanoscale variability. These and other unique aspects of these structures are embodied in an overall concept of lab-in-wire, or similar self-assembled structures, extending our previous concept of lab-in-fibre from the micro domain into the nano domain.