All three players started the opening game against Wales before missing Sunday's 44-8 defeat by England at Twickenham.
Prop Atonio, who travelled to London with the team, has been struggling with a knee injury, while Fofana had a thigh strain and Medard needed an MRI on a shoulder problem.
Brunel has chosen to stick with the same squad that featured in the first two matches of the tournament, despite facing criticism for a dismal defensive performance against England.
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With the title already well out of their reach, Les Bleus must now avoid defeat against Scotland at the Stade de France on Feb. 23 if they do not want to play a 'wooden spoon' clash in Rome against Italy in their last outing.

Full squad

Forwards: Jefferson Poirot (Bordeaux-Bègles), Dany Priso (Stade Rochelais), Guilhem Guirado (c) (RC Toulon), Pierre Bourgarit (Stade Rochelais), Camille Chat (Racing 92), Dorian Aldegheri (Stade Toulousain), Uini Atonio (Stade Rochelais), Demba Bamba (CA Brive), Felix Lambey (Lyon OU), Sebastien Vahaamahina (ASM Clermont Auvergne), Paul Willemse (Montpellier), Gregory Alldritt (Stade Rochelais), Yacouba Camara (Montpellier), Arthur Iturria (ASM Clermont Auvergne), Wenceslas Lauret (Racing 92), Louis Picamoles (Montpellier), Fabien Sanconnie (Racing 92)
Backs: Antoine Dupont (Stade Toulousain), Morgan Parra (ASM Clermont Auvergne), Baptiste Serin (Bordeaux-Bègles), Anthony Belleau (RC Toulon), Camille Lopez (ASM Clermont Auvergne), Mathieu Bastareaud (RC Toulon), Geoffrey Doumayrou (Stade Rochelais), Wesley Fofana (ASM Clermont Auvergne), Romain Ntamack (Stade Toulousain), Gael Fickou (Stade Français), Yoann Huget (Stade Toulousain), Maxime Medard (Stade Toulousain), Damian Penaud (ASM Clermont Auvergne), Thomas Ramos (Stade Toulousain) (Reporting by Hardik Vyas in Bengaluru Editing by Christian Radnedge)
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