Dichroic organic films have found a broad application in various optoelectronic devices. One efficient method for the production of thin dichroic films is the deposition of the film onto aligning polymer surface. Scientists propose different explanations concerning the mechanisms of the molecules aligning. Here, we report the aligning of squaraine (Sq) molecules on the different aligning polymer surfaces, independent from the morphology of the Sq deposits. Aligned polytetrafluoroethylene (PTFE) layers were produced by either unidirectional hot friction transfer or by PTFE decomposition in vacuum with the activation of the gas by accelerated electrons and the consequent unidirectional rubbing with a cloth. Sq films grown on the aligned PTFE surfaces and on the nanostructured polycarbonate (PC) surfaces were found to exhibit dichroic optical absorption spectra. Despite different shape and orientation of the Sq crystals on the PTFE and the PC surfaces, the absorption of polarized light was shown to exhibit one pattern. Variations in the morphology of Sq films on different surfaces were explained by the competitive participation of different growth mechanisms, which depended on the properties of the deposited compound, the aligning layer and the growth conditions. The PTFE aligning layers can be useful in organic electronics due to low-temperature processing. Graphic abstract