Filmer's father died in November 1629 and Filmer, as the oldest child, took over his father's manor house and estate. He became a Justice of the Peace and an officer of the county militia in the 1630s. Filmer's eldest son Sir Edward was active in opposing the Long Parliament and Filmer stood surety for £5000 for the release of his friend Sir Roger Twysden, who had been imprisoned for his part in the Kentish petition. The Parliamentary army looted his manor house in September 1642. By the next year his properties in Westminster and Kent were being heavily taxed to fund the Parliamentary cause. Filmer was investigated by the county committee on suspicion of supporting the King, though no firm evidence was uncovered. Filmer asked the investigators to note "how far he hath binn from medling on either side in deeds or so much as words." One of his tenants claimed that Filmer had hidden arms for the Royalists, although this was apparently a false charge. Perhaps for that reason, Filmer was imprisoned for some years in Leeds Castle and his estates were sequestered.