Dopant species can interact in different ways with interfaces, layers of varied microstructures, and with extended-defects. An understanding of such interactions is relevant to semiconductor processing and device-fabrication. In this study, the behavior of phosphorus-implanted silicon wafers was characterized using transmission electron microscopy (TEM), for as-implanted as well as post-implant rapid thermal-anneal (RTA) conditions. The top layers of as-implanted wafers were found to be amorphized. A correlation was seen between the presence of the amorphous-to-crystalline silicon interface and a drop in phosphorus concentrations in depth-profiles obtained using SIMS (secondary-ion mass-spectrometry). Reasons for the drop in concentration are explored, one of which is a higher diffusivity for phosphorus in amorphous silicon than in crystalline silicon. The top layers of wafers subjected to a RTA had recrystallized. A band of extended defects was present in the vicinity of the original amorphous-to-crystalline silicon interface. A correlation was seen between the presence of these defects and a secondary peak in phosphorus concentrations (in depth profiles) obtained using SIMS. These effects are explained in terms of gettering of phosphorus to the extended-defects. The band of extended-defects consists of dislocation loops, point-defect clusters, and extended dislocations that arise due to coalescing of point defects followed by annealing of the resulting extended-defects. The point-defects themselves arise from the implantation.