Flexible macromolecule poly(tetrafluoroethylene) (PTFE) has shown its unique capacity for crystallization and molecular orientation: it forms long extended-chain crystalline whiskers and well orients in its thin films. Formation of the highly oriented structure is essential for oriented growth of materials and for study of the crystal, having a great impact on materials science and engineering. Like laser ablation, synchrotron radiation (SR) can be used to directly etch materials without using any chemicals, offering a simple and versatile method for forming thin films. Using Fourier transfer infrared spectroscopy, the thin PTFE films deposited by the SR etching were found to have polymer chains highly oriented with molecular axes aligned to be perpendicular to substrate surface, whereas the molecular axes align to be parallel to the substrate surface in the films deposited by the laser ablation. Studying with mass spectrometry and X-ray photoelectron spectroscopy, we come to understand this change in molecular orientation by finding molecular oligomers of perfluoro-n-alkanes as photofragments involved in the SR case.