Filtering (or thinning) is an informal game term. It means to remove useless or situationally-irrelevant cards from your deck, generally by searching your deck for them. You've "filtered" out cards, meaning that you have a "thinner" deck composed only of the cards you actually want to draw. Typically, players will want to filter Free Peoples cards out of their decks as quickly as possible, to have hands full of Shadow cards for the important late-game turns.
One of the strongest filter strategies in the game "Horn filter", a strategy from Expanded using Erkenbrand's Horn (18R96). You pack your deck full of Followers, then use the Horn over and over to put them all into play. This is especially powerful in conjunction with Gamling, Defender of the Hornburg (11R147) to download it on the first turn, and New Chapter (13U154), to heal the exertions from using the Horn.