Layers of carbocyanine polymethine dyes were studied to evaluate the effect exerted by the molecular structure and thickness of a layer on its component composition. Thin layers contain cis-monomers of different structure as major form. The number of types of cis-isomers decreases and the relative concentration of the all-trans isomers increases with increasing thickness. As the electron-donating ability of end groups and the chain length grow, the number of stereoisomers of different types increases. It was concluded that the equilibrium stereoisomeric composition of the layer is determined by degree of asymmetry, which is induced in the intramolecular electron density distribution by the interaction with substrate. We developed the model for rearrangement of layer by heating and photoexcitation. Reversible changes in the component composition are due to the stereoisomerization upon rotation of a molecule fragment around the second polymethine chain bond and irreversible changes, due to the change in asymmetry of the electron density distribution owing to irreversible spatial reorientation of layer components. The spatial reorientation of layer components is determined by stereoisomerization upon rotations around the central bonds.© (2010) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.