The helical supramolecular structure of cholesteric liquid crystalline (LC) films predetermines their outstanding optical properties and the unique nanostructure of their surface. The introduction of photochromic dopants in these films opens up an interesting possibility for creation of smart cholesteric materials with photocontrollable optical and photovariable surface properties. Using atomic force microscopy (AFM), we performed in situ measurements of the surface topography of cyclosiloxane LC cholesteric oligomer films during the cholesteric helix twisting caused by their preliminary ultraviolet (UV) irradiation. A chiral-photochromic isosorbide-based dopant was introduced in the films to control the cholesteric helix pitch by UV-irradiation. The initial films are characterized by planar texture with the presence of focal conic domains having the double-spiral relief on their surface. UV-irradiation of these films leads to the cholesteric helix twisting resulting in a decrease in the surface relief period, and the enlargement of defect areas between the domains. The detailed mechanisms of the rearrangement of the film surface structure due to the cholesteric helix twisting are suggested. They include the rotation and displacement of cholesteric layers in the bulk, and the nucleation of new ones at the surface in defect regions.