We investigate the molecular and microdomain structure of ferroelectric poly(vinylidene fluoride-co-trifluoroethylene) P(VDF-TrFE) copolymer thin films spin-coated on bare and self-assembled monolayers (SAMs)-modified An substrates. The two types of films display similar crystal morphologies with edge-on needlelike shaped crystalline microdomains. They have, however, a different structure depending on the substrate. When the P(VDF-TrFE) films are deposited on a bare, unmodified An surface, the P(VDF-TrFE) films preferentially have a (110) contact plane with the substrate but a (100) contact plane when deposited on the An surface modified by SAMs. The polar b-axis, along which the ferroelectric polarization is oriented, is therefore tilted to the film (and substrate) surface normal at 30 and 90 degrees, respectively. In particular, the orientation of the polar b-axis tilted at some 90 degrees to the normal of the polymer films on a CH3 terminated SAM modified Au surface explains the smaller remanent polarization at low initial electrical bias.