Two different polymorphic forms of free base phthalocyanine films have been grown on glass substrates by ultrahigh vacuum organic molecular beam deposition. Postgrowth annealing of films grown at room temperature leads to transformation from the alpha to the beta(1) phase. The effects of annealing lead to a number of transition states whose morphological, structural, and spectroscopic properties can be identified using atomic force and optical interference microscopy, X-ray diffraction, and Raman and electronic absorption spectroscopy. Detailed morphological studies indicate that the transition occurs via a discrete number of nucleations and is preceded by an elongation of the alpha crystallites. Quantitative analysis of the crystallites and domain size shows that the individual beta(1) crystals grow but are confined to domains of similar orientation. The film thickness plays a critical role and three regimes have been identified. The alpha --> beta(1) transformation is only complete for films thicker than similar to 940 Angstrom, and thick films lead to a higher degree of orientation and larger domains.