In various embodiments of a method for filling root canal spaces, the root canal spaces are cleaned and irrigated, for example, by any suitable endodontic procedure, and the irrigating liquid is not removed from the canal spaces prior to filling. In some embodiments, a hydrophobic filler material is introduced into the root canal spaces while they are filled with liquid. As the canal spaces are filled, the hydrophobic filler material displaces the liquid and drives it out of the canal spaces, towards the crown of the tooth, where it can be removed. The hydrophobic filler material may comprise magnetically responsive particles having a hydrophobic surface coating that are compacted into the root canal spaces by application of a magnetic force field. In other embodiments, hydrophilic filler material in a flowable phase is introduced into the canal spaces where it partly displaces and partly absorbs the irrigating liquid before solidifying.