We conducted research on controlling arrays of functional organic molecules from the viewpoint of self-assembly. Molecular thin films were fabricated and their structures were examined by using a Scanning Tunneling Microscope (STM). Molecules used in the experiments are derivatives of porphyrin. Tertiary-butyl-phenyl-porphyrin (TBPP) and tertiary-butyl-phenyl-porphyrin-CN (TBPP-CN) were mainly used. STM images of the molecular arrays of TBPP and TBPP-CN appeared quite different. Infrared Reflection Absorption Spectroscpopy (IRAS) spectra of bulky structures were obtained.