Special spectrum regions, like around the annihilation peak at 511 keV, the boron peak at 478 keV, the Ge-triangles, as well as complicated multiplets or heavily distorted intense peaks require special attention when evaluating Prompt-gamma Activation Analysis (PGAA) spectra. A computer code and the related analytical practice of the Budapest PGAA facility is presented to improve the spectroscopy of these cases beyond the past practice relying on the well-known Hypermet-PC software.