During the August putsch of 1991 Filatov headed the defence staff of the White House.

From January 1993 to January 1996, Filatov was the head of the Presidential Administration of Russia, as well as the chairman of the Expert and Analytical Council under the President of Russia and the chairman of the Presidential Commission on state awards in the field of literature and art.

In 1996, Filatov left the state service and he was appointed deputy head of Boris Yeltsin's reelection headquarters.

He headed the Public Movement to Support the President (ODOPP) and later the All-Russian Coordination Council (OKS), which was in charge of 1996 and 1997 election campaigns of Yeltsin-appointed governors.

In April 2006, he became the Chairman of the Expert Council of the "Attention" Foundation, which held the first ADHD-themed forum in Russia.