For the first time, AFM study of laser induced surface deformation and crater (holes) formation in liquid crystalline (LC) azobenzene-containing photochromic polymer systems was performed. Special set up including combination of polarizing optical, atomic force microscopies and a possibility of irradiation with a highly focused laser beam (532 nm) was used for these investigations. Films of the nematic azobenzene-containing polyacrylate polymer and the cholesteric mixture prepared by doping of this polymer with the chiral dopant were investigated. Focused laser beam irradiation results in the crater formation formed due to a mass-transfer outside center of beam. Depth of these craters lies in the range of tens of nanometers and increases by prolongation of irradiation time. It is found that this phenomenon takes place only for thick (5–10 μm) films, whereas these phenomena do not take place for the thin spin-coated films. For nematic and cholesteric films the rate of the crater formation, their depth and diameter are the same; that means the chirality of the systems has no influence on kinetics and the depth of photoinduced craters. It is shown, that for the nonaligned LC-films no preferable directed mass transport nearby photoinduced holes was found, but in the case of the uniaxially aligned nematic polymer films the mass-transport occurs only in direction along LC-director and does not depend on the laser polarization direction.