We investigated the effect of CW radiation at 0.6 THz on pathological protein aggregates in the form of amyloid fibrils, i.e. ordered protein complexes linked to neurodegenerative diseases such as Parkinson's and Frontotemporal Dementia. To monitor the effect of THz irradiation we exploited mid-infrared (mid-IR) vibrational spectroscopy in the amide-I band range, whose lineshape is known to depend on the protein conformation and on how proteins arrange into ordered supramolecular complexes such as fibrils.