When the verdict against Filbert was confirmed as legally binding, the former head of EK 9 had already spent just over four years in prison. He was now facing a life sentence in West Berlin's Tegel Prison (Strafanstalt Tegel, today Justizvollzugsanstalt Tegel) at 39 Seidelstraße, where he was given the prisoner number 1251/63. At this time in the Federal Republic of Germany, a distinction was made between different types of imprisonment: penal servitude (Zuchthaus); prison (Gefängnis); confinement (Einschließung); and detention (Haft). Filbert had received a sentence of life in Zuchthaus. The Zuchthaus had emerged as a form of incarceration in the Netherlands and northern Germany in the late sixteenth and early seventeenth centuries. It combined the twin purposes of chastisement through labour and the opportunity for re-socialisation. In June 1969, the distinction between different types of imprisonment was abolished in the Federal Republic of Germany, and the Zuchthaus along with it. Thus, life sentences in Zuchthaus and in Gefängnis were now both altered to the more generic sentence of ‘life imprisonment’ (lebenslange Freiheitsstrafe). This alteration to the Criminal Code also applied to sentences already imposed but not yet, or not yet fully, served. Thus, Filbert's own sentence of life in Zuchthaus was affected by these changes. The provisions came into effect on 1 April 1970.

On 15 January 1964, the Justus Liebig University in Giessen resolved to strip Filbert of the Doctor of Laws title he had obtained on 27 February 1935, as it considered Filbert unworthy of using the doctor title in light of the judgement passed against him by the Regional Court in Berlin. On 12 February 1964, the university wrote to Filbert to inform him of its decision. On 2 March, in a four-and-a-half-page handwritten letter to the university, Filbert filed an objection. In his letter he claimed that he had been appointed head of EK 9 as retribution for the conduct of his brother Otto, who had been imprisoned by the regime for political reasons. He furthermore claimed that refusal to carry out the mass shootings against Jews and other Soviet citizens had been punishable by death. He claimed thus to have had no choice but to commit the crimes of which the Regional Court in Berlin had found him guilty. As he had throughout the legal proceedings against him, he again pleaded superior orders.