The formation of high-quality organic thin films with low defect densities and good lateral ordering is essential for many electronic and optical technologies. Here, electrochemically fabricated thin films of conducting and superconducting organic charge-transfer salts are examined using AFM, which reveals revealing frictional anisotropy between domains in the films. The number and size of the domains can be reduced through an ''electrochemical annealing'' process. The role of epitaxy in domain formation and the influence of domain size on the dynamics of annealing are discussed.