Molecular transport through nanoscale pores in films, membranes and wall structures is of fundamental importance in a number of physical, chemical and biological processes(1-6). However, there is a lack of experimental methods that can obtain information on the structure and orientation of the molecules as they pass through the pore, and their interactions with the pore during passage. Imaging with a transmission electron microscope is a powerful method for studying structural changes in single molecules as they move(7,8) and for imaging molecules confined inside carbon nanotubes(9). Here, we report that such imaging can be used to observe the structure and orientation of a hydrocarbon chain as it passes through nanoscale defects in the walls of a single-walled carbon nanotube to the vacuum outside, and also to study the interactions between the chain and the nanopore. Based on experiments at 293 K and 4 K we conclude that the major energy source for the molecular motions observed at 4 K is the electron beam used for the imaging.