Carbon-Based Anatomy EP is composed of six previously unheard tracks. However, the song "Carbon-Based Anatomy" is a reinterpretation of an older unreleased Æon Spoke single, "Homosapien". This was also done on Cynic's last LP, Traced in Air, as the track "Integral Birth" was an interpretation of Æon Spoke's "When Sunrise Skirts the Moor." The artwork was done by Roberto E. Venosa, the artist who was responsible for all previous Cynic artworks. Venosa died shortly before the release of Carbon-Based Anatomy.
Three of six tracks are short, ambient-oriented pieces ("Amidst the Coals", "Bija!", and "Hieroglyph"), and represent an unprecedented musical direction for Cynic. Since the two previous full-time band members, Tymon Kruidenier and Robin Zielhorst, left the band, all guitar parts for this EP were recorded by Paul Masvidal. Bass parts were composed and recorded by Sean Malone, who had recorded on every Cynic release up to date, except for 2010's Re-Traced.
- "Amidst the Coals" – 2:11
- "Carbon-Based Anatomy" – 6:24
- "Bija!" – 2:27
- "Box Up My Bones" – 5:32
- "Elves Beam Out" – 3:59
- "Hieroglyph" - 2:28
- Paul Masvidal – vocals, guitar, guitar synth
- Sean Reinert – drums, percussion, keyboards
- Sean Malone – bass
- Amy Correia – female vocals
- John Hiler – mixing, engineering
- Maor Appelbaum – mastering engineer