Tim DiGravina of Allmusic said the album was "hard to recommend". He went on to say while it did contain one of the band's best songs, "Deep Down Trauma Hounds", much of the album was ambient and fragmentary. He concluded by saying the album was primarily recommendable to die hard fans.
Cleanse Fold and Manipulate is a cyclical album, the end of the track 10, "Epilogue" segues into the beginning of track 1, "First Aid."
In response to the cover's source image by Gilmore: "It is an image from the original 1960's movie of Village Of The Damned. There is a little tongue-in-cheek history behind using that image as the manager for Images In Vogue, a band that C. Key used to be in before Skinny Puppy, was a former child model from England and had a role in the movie. But the face on the cover was another child actor from the movie."
The song "The Mourn" is based on the extreme horror Guinea Pig film Flower of Flesh and Blood, and when it was written, they thought it was real. Footage from the movie has since been used in their live shows.