We investigate the role of conformational disorder and intermolecular interactions on the electronic structure of amorphous clusters of polyfluorenes. Classical molecular dynamics simulations are used to determine probable molecular geometries and chain packing, and first-principles density functional theory calculations are employed to determine electronic structure and orbital localization properties. Intramolecular and intermolecular effects are disentangled by contrasting results for densely packed oligomer clusters and for ensembles of isolated oligomers with the same intramolecular geometries. Our simulations show that intermolecular disorder allows for nearly planar configurations of interacting fluorenes compared to the isolated molecules. This rationalizes the experimentally detected formation of the planar crystalline morphologies that frequently accompany twisted glassy configurations in fluorene films. The energy gap (HOMO-LUMO gap) significantly decreases for planar configurations. The electron and hole orbital energies are strongly dependent on both torsional angles and intermolecular interactions. This leads to strong localization of electronic states in amorphous polymer aggregates, which is analyzed by examining the respective orbital participation ratios. Notably, the energies of unoccupied levels show stronger dependence on the conformational disorder, compared to that of occupied levels. This results in the more probable formation of trap states near the edge of the conduction band than near the valence band.