Adsorption processes of thiolated cyclodextrins onto the self-assembeled monolayers of octanethiol formed on Au(111) substrates were investigated with a scanning tunneling microscope (STM). Our results revealed that the exchange of alkanethiolate molecules with the thiolated cyclodextrins occurred preferentially at the boundaries of the domains of a c(4×2) structure. Moreover, the adsorbed thiolated cyclodextrins were found to form one-dimensional chain structures. Our approach presented here provides a way to organize ordered structures of bulky molecules on solid substrates.