Fluorinated single-walled carbon nanotubes (F-SWNTs) form important intermediates in SWNT sidewall functionalization leading to a variety of materials and biological applications. By simulating the infrared (IR) signals for the 1,2- and 1,4-addition structures, in which fluorine atoms are arranged in ortho or para positions, respectively, on the aromatic skeleton of the (10, 10) SWNT surface, we identify peaks that are unique to each structure. Our full molecular dynamics simulations show that the [-C(sp(3))-C(sp(3))-] collective vibrational peak at 400 cm(-1) is optically active only in the 1,2-isomer, while the 1300 cm(-1) band arising due to the F-C(sp(3)) stretching motion coupled with the neighboring C(sp(2)) atoms is seen in the IR spectrum of only the 1,4-isomer. The reported results suggest simple and clear experimental means for distinguishing between the two fluorinated structures and provide a valuable tool for controlled SWNT sidewall functionalization.