Best-performing organic photovoltaic devices rely on nanostructured active layer morphology to have better hole-electron separation and their extraction from the active layer to respective extraction electrode. Although much progress has been made in designing new organic molecules, rational control over active layer morphology remains a central challenge. In this article, we have presented a control means to improve the morphology of active layer and the degree of carrier transportation from the active layer ZnPc to Electron Transportation Layer (ETL) SnO2 using variable self-assembly behavior of ZnPc molecules with assistance of annealing. Post processed annealed sample at 290 degrees C shows better photo response compared to as-deposited sample. Structural and electrical studies supports the formation of columnar shape nanostructures in the active layer on annealing results in better hole-electron separation at the interface with ETL favored by better extraction of charge carrier to their respective electrode. Annealing resulted in enhancement of mobility from 1 x 10(-7) m(2) V-1 s(-1) for as-deposited sample to 1.7 x 10(-6) m(2) V-1 s(-1) for 290 degrees C annealed sample with corresponding reduction of trap concentration from 3.6 x 10(26) m(-3) to 2.0 x 10(26) m(-3) because of ordered molecular stacking of ZnPc molecules into columnar shape nanostructure favored by heat treatment.