Using the Wordnet dictionary I encountered the following definitions:

The verb riffle has 4 senses (first 1 from tagged texts) 1. (1) flick, ruffle, riffle -- (twitch or flutter; "the paper flicked") 2. flick, flip, thumb, riffle, leaf, riff -- (look through a book or other written material; "He thumbed through the report"; "She leafed through the volume") 3. ripple, ruffle, riffle, cockle, undulate -- (stir up (water) so as to form ripples) 4. riffle -- (shuffle (playing cards) by separating the deck into two parts and riffling with the thumbs so the cards intermix)

It seems that "riffling" is a bit less sinister than rifling through the Monastery - it implies going through pages, etc. (or cards, as in #4 above)