We describe the results of electrophoretic deposition characteristics of a conjugated polymer, polydiacetylene (PDA), that reveal film forming behavior, polymerization effects, pattern transfer capabilities, and fluorescence based thermo/mechano-responsive features of the deposited layer. The electric field applied in a two electrode system promotes the oriented motion of diacetylene (DA) supramolecules in aqueous solution in a direction that is determined by the charge polarities of tailorable pendant groups on the DA monomers. Through this mechanism, electrophoretic deposition of DA supramolecules on a conductive layer takes place to yield vesicular clustered aggregates with continuous leaf-like morphologies. In addition, unusual conformational changes of the DA monomers during the deposition result in the formation of polymerized blue colored PDAs on the working electrode. Based on these properties, selective deposition of the supramolecules on pre-patterned templates and consequent pattern transfer to a flexible substrate can be utilized to fabricate PDA-based microarray sensors. The chromatic change of the vesicles induced by an applied mechanical stress during pattern transfer is found to be dependent on the side groups of the DA monomers. Owing to inherent non-fluorescence to fluorescence transition features of PDA supramolecules occurring as a response to thermal perturbations, electrophoretically deposited PDA vesicles are employed to monitor the temperature of a heat dispensing micro-heater device.