Atomic force microscopy (AFM) and Fourier transform infrared (FTIR) spectroscopy were used to investigate the structure and surface morphology of an azobenzene-containing Langmuir-Blodgett (LB) film. Molecularly-resolved AFM images revealed a slightly distorted monoclinic crystal structure with a unit cell of a = 6.08 +/- 0.03 Angstrom, b = 5.67 +/- 0.03 Angstrom, and an angle of 55 degrees +/- 1 degrees between these two in-plane axes. An average molecular orientation of 39 degrees +/- 2 degrees with respect to the film surface normal was determined using FTIR spectra. Using polarized UV excitation of the azobenzene-containing LB film, selective trans-to-cis photoisomerization was obtained and was characterized by the polarized UV-visible spectra. Clear morphological differences between films subjected to unpolarized vs polarized UV illumination were observed with in situ AFM. Domains on the order of 10 nm in diameter or less are thought to be associated with the photoisomerization process.