We report the results of a systematic study for the elucidation of detailed molecular arrangements in Disperse Red 1(DR1) films prepared by electric field assisted physical vapor deposition (EFA-PVD) method on ITO substrate with varied field strength. Aside from confirming the periodic molecular chain structure reported previously, the electric field induced increase of crystallinity is corroborated by the enhanced crystalline appearance in the SEM images of the films deposited with increased applied field up to a certain limit. The optical spectroscopic measurements in both the transmission and reflection modes clearly show that instead of the anti-parallel polar arrangement found previously in films deposited without the applied electric field, it is the parallel arrangements of molecular aggregates that are found in the currently produced films which offer its potential application for the generation of second harmonic (SH) light. A detailed analysis of the additional FTIR-RAS data further reveals the formation of hydrogen bondings in the head-to-tail stacking along the molecular chain responsible for its periodic structure, as well as those between the DR1 hydroxyl end groups and the oxide components in the ITO substrate which provides the molecular immobilizing or anchoring mechanism for the deposited films. This explains in turn, the improved film stability and the formation of the highly desirable parallel polar arrangement of the DR1 molecules in the deposited films, promising for SHG and other related nonlinear optical (NLO) applications.