Near-field scanning optical microscopy (NSOM) and scanning force microscopy have been employed to spatially resolve the complex morphologies, spectroscopy, and charge transfer induced fluorescence quenching efficiencies of a (perylene phenethylimide)/(titanyl phthalocyanine) bilayer (PPEI/TiOPc). The PPEI/TiOPc bilayer is a typical example of a n-like/p-like molecular semiconductor heterojunction, which is a common component in photocells, LEDs, and other devices. NSOM-polarized fluorescence and transmission data - and separate bulk X-ray diffraction and spectroscopic measurements - on PPEI/TiOPc bilayers and PPEI and TiOPc single layers has lend to a nanoscopic and mesoscopic picture of how vacuum deposition and subsequent solvent-vapor-annealing controls the local structure of these films. The layers and bilayers are highly organized, containing localized crystalline regions which are preferentially oriented relative to the substrate and PPEI/TiOPc interface. In highly annealed bilayers, only a small fraction of the area of the interface makes good contact between the bilayers, and the contact regions are less than 100 nm(2) in most cases. The consequences of the observed morphology on the charge separation efficiencies at the interface is examined. It is shown that exciton migration both perpendicular and parallel to the molecular interface are involved in the charge separation mechanism. Extended methylene chloride, solvent-vapor-annealing of PPEI films produces long needle-like PPEI crystals with a range of sizes, as follows: width (50-200 nm), length (1000-2000 nm), and height (50-200 nm). Annealing of the TiOPc yields nanocrystallites that are preferentially oriented relative to the interface with a height in the range of 10-100 nm and widths in the range of < 10 nm to 30 nm.